Back to Long Tests report for BioC 3.20 |
This page was generated on 2024-06-29 23:55 -0400 (Sat, 29 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4408 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 6/32 | Hostname | OS / Arch | CHECK | |||||||
biodbChebi 1.11.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
To the developers/maintainers of the biodbChebi package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: biodbChebi |
Version: 1.11.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbChebi_1.11.0.tar.gz |
StartedAt: 2024-06-29 16:01:07 -0400 (Sat, 29 Jun 2024) |
EndedAt: 2024-06-29 16:04:28 -0400 (Sat, 29 Jun 2024) |
EllapsedTime: 200.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biodbChebi.Rcheck |
Warnings: 0 |
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbChebi) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbChebi") biodb.INFO [2024-06-29 16:01:42.575][biodb::testContext] biodb.INFO [2024-06-29 16:01:42.578][biodb::testContext] ******************************************************************************** biodb.INFO [2024-06-29 16:01:42.579][biodb::testContext] Test context - Generic long tests biodb.INFO [2024-06-29 16:01:42.580][biodb::testContext] ******************************************************************************** biodb.INFO [2024-06-29 16:01:42.580][biodb::testContext] biodb.INFO [2024-06-29 16:01:42.586][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0. biodb.DEBUG[2024-06-29 16:01:42.587][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2024-06-29 16:01:42.593][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-29 16:01:42.594][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-06-29 16:01:42.595][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-06-29 16:01:42.595][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.598][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-06-29 16:01:42.612][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-06-29 16:01:42.613][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.616][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-06-29 16:01:42.616][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-06-29 16:01:42.617][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.619][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-06-29 16:01:42.620][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-06-29 16:01:42.621][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-06-29 16:01:42.622][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.634][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-06-29 16:01:42.634][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-06-29 16:01:42.635][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-06-29 16:01:42.636][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.638][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-06-29 16:01:42.638][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-06-29 16:01:42.639][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.641][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-06-29 16:01:42.642][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-06-29 16:01:42.643][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-06-29 16:01:42.643][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.645][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-06-29 16:01:42.646][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-06-29 16:01:42.647][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.649][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-06-29 16:01:42.649][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-06-29 16:01:42.650][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-06-29 16:01:42.651][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.653][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-06-29 16:01:42.653][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-06-29 16:01:42.654][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-06-29 16:01:42.655][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-06-29 16:01:42.656][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-06-29 16:01:42.656][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-06-29 16:01:42.657][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.659][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-06-29 16:01:42.660][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-06-29 16:01:42.661][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.663][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-06-29 16:01:42.663][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-06-29 16:01:42.664][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.666][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-06-29 16:01:42.667][self$set] Set key offline to FALSE. biodb.DEBUG[2024-06-29 16:01:42.667][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.669][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-06-29 16:01:42.670][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-06-29 16:01:42.671][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.673][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-06-29 16:01:42.674][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-06-29 16:01:42.674][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.677][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-06-29 16:01:42.677][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-06-29 16:01:42.695][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-06-29 16:01:42.696][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.698][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-06-29 16:01:42.699][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-06-29 16:01:42.700][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-06-29 16:01:42.701][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.705][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-06-29 16:01:42.732][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.744][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-06-29 16:01:42.745][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.746][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-29 16:01:42.747][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.748][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-29 16:01:42.749][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.749][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-29 16:01:42.750][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-06-29 16:01:42.751][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-29 16:01:42.752][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.753][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-06-29 16:01:42.753][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-29 16:01:42.754][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.755][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.756][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-06-29 16:01:42.756][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-06-29 16:01:42.756][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-06-29 16:01:42.756][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-06-29 16:01:42.756][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-06-29 16:01:42.757][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-29 16:01:42.757][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-29 16:01:42.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-29 16:01:42.759][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-29 16:01:42.760][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-29 16:01:42.760][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-29 16:01:42.761][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-29 16:01:42.762][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.763][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-29 16:01:42.763][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-29 16:01:42.764][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.765][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.766][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-06-29 16:01:42.767][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.768][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-06-29 16:01:42.768][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.769][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-29 16:01:42.770][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.771][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-29 16:01:42.772][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.772][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-29 16:01:42.773][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-06-29 16:01:42.774][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-29 16:01:42.775][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.775][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-06-29 16:01:42.776][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-29 16:01:42.777][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.777][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.778][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-06-29 16:01:42.778][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-06-29 16:01:42.778][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-06-29 16:01:42.778][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-06-29 16:01:42.778][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-06-29 16:01:42.779][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-29 16:01:42.780][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-29 16:01:42.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-29 16:01:42.781][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-29 16:01:42.782][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-29 16:01:42.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-29 16:01:42.783][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-29 16:01:42.784][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.785][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-29 16:01:42.786][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-29 16:01:42.786][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.787][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.788][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-06-29 16:01:42.789][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.790][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-06-29 16:01:42.791][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.791][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-29 16:01:42.792][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.793][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-29 16:01:42.793][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.794][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-29 16:01:42.795][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-06-29 16:01:42.795][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-29 16:01:42.801][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.801][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-06-29 16:01:42.802][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-29 16:01:42.803][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.803][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.804][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.805][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-29 16:01:42.805][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-29 16:01:42.806][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-29 16:01:42.807][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-29 16:01:42.807][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-29 16:01:42.808][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-29 16:01:42.809][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-29 16:01:42.809][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.810][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-29 16:01:42.811][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-29 16:01:42.811][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.812][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.813][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-06-29 16:01:42.814][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.815][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-06-29 16:01:42.815][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.816][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-29 16:01:42.817][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.818][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-29 16:01:42.819][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.819][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-29 16:01:42.820][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-06-29 16:01:42.821][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-29 16:01:42.821][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.822][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-06-29 16:01:42.823][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-29 16:01:42.824][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.825][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-29 16:01:42.825][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.826][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-29 16:01:42.827][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-29 16:01:42.827][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-29 16:01:42.828][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-29 16:01:42.829][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-29 16:01:42.830][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-29 16:01:42.830][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-29 16:01:42.831][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.832][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-29 16:01:42.833][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-29 16:01:42.833][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-29 16:01:42.834][self$setPropertyValue] biodb.DEBUG[2024-06-29 16:01:42.837][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-29 16:01:42.838][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.839][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.843][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.846][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.849][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.852][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.855][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.858][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.862][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.865][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.868][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.871][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.875][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.878][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.881][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.885][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.888][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.891][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:42.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:42.895][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-06-29 16:01:42.898][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-06-29 16:01:42.899][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-06-29 16:01:42.900][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-06-29 16:01:42.901][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-06-29 16:01:42.902][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-06-29 16:01:42.903][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-06-29 16:01:42.905][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-06-29 16:01:42.906][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-06-29 16:01:42.907][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-06-29 16:01:42.908][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-06-29 16:01:42.908][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-06-29 16:01:42.909][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-06-29 16:01:42.910][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-06-29 16:01:42.912][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-06-29 16:01:42.913][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-06-29 16:01:42.914][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-06-29 16:01:42.915][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-06-29 16:01:42.916][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-06-29 16:01:42.917][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-06-29 16:01:42.918][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-06-29 16:01:42.919][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-06-29 16:01:42.920][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-06-29 16:01:42.921][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-06-29 16:01:42.922][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-06-29 16:01:42.924][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-06-29 16:01:42.925][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-06-29 16:01:42.926][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-06-29 16:01:42.927][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-06-29 16:01:42.928][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-06-29 16:01:42.929][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-06-29 16:01:42.930][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-06-29 16:01:42.931][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-06-29 16:01:42.932][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-06-29 16:01:42.934][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-06-29 16:01:42.935][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-06-29 16:01:42.936][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-06-29 16:01:42.937][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-06-29 16:01:42.938][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-06-29 16:01:42.939][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-06-29 16:01:42.940][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-06-29 16:01:42.941][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-06-29 16:01:42.942][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-06-29 16:01:42.943][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-06-29 16:01:42.944][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-06-29 16:01:42.949][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-06-29 16:01:42.950][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-06-29 16:01:42.951][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-06-29 16:01:42.952][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-06-29 16:01:42.953][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-06-29 16:01:42.954][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-06-29 16:01:42.955][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-06-29 16:01:42.956][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-06-29 16:01:42.957][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-06-29 16:01:42.958][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-06-29 16:01:42.959][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-06-29 16:01:42.960][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-06-29 16:01:42.961][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-06-29 16:01:42.962][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-06-29 16:01:42.963][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-06-29 16:01:42.964][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-06-29 16:01:42.965][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-06-29 16:01:42.966][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-06-29 16:01:42.967][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-06-29 16:01:42.968][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-06-29 16:01:42.969][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-06-29 16:01:42.970][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-06-29 16:01:42.971][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-06-29 16:01:42.972][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-06-29 16:01:42.973][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-06-29 16:01:42.974][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-06-29 16:01:42.975][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-06-29 16:01:42.976][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-06-29 16:01:42.977][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-06-29 16:01:42.978][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-06-29 16:01:42.979][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-06-29 16:01:42.980][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-06-29 16:01:42.981][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-06-29 16:01:42.982][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-06-29 16:01:42.983][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-06-29 16:01:42.984][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-06-29 16:01:42.985][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-06-29 16:01:42.986][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-06-29 16:01:42.991][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-06-29 16:01:42.992][initialize] This is biodb version 1.13.0. biodb.DEBUG[2024-06-29 16:01:42.994][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-29 16:01:42.995][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:42.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:42.996][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:42.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.000][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.005][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.009][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.014][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.018][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.023][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.027][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.032][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.036][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.040][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.045][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.050][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.055][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.059][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.064][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.069][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.074][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-29 16:01:43.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:43.079][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/definitions.yml". biodb.DEBUG[2024-06-29 16:01:43.091][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2024-06-29 16:01:43.092][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-29 16:01:43.093][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-06-29 16:01:43.094][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-29 16:01:43.094][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-29 16:01:43.095][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-29 16:01:43.096][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-29 16:01:43.097][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-06-29 16:01:43.097][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2024-06-29 16:01:43.098][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2024-06-29 16:01:43.099][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-29 16:01:43.099][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-29 16:01:43.100][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2024-06-29 16:01:43.101][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-29 16:01:43.102][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2024-06-29 16:01:43.102][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2024-06-29 16:01:43.102][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2024-06-29 16:01:43.102][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2024-06-29 16:01:43.102][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2024-06-29 16:01:43.102][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2024-06-29 16:01:43.102][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2024-06-29 16:01:43.102][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2024-06-29 16:01:43.102][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2024-06-29 16:01:43.102][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2024-06-29 16:01:43.102][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2024-06-29 16:01:43.103][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-06-29 16:01:43.103][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-06-29 16:01:43.103][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-06-29 16:01:43.103][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-06-29 16:01:43.104][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-06-29 16:01:43.105][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-29 16:01:43.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-29 16:01:43.106][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-29 16:01:43.107][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-29 16:01:43.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-29 16:01:43.108][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-29 16:01:43.109][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:43.109][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2024-06-29 16:01:43.109][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-29 16:01:43.110][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-29 16:01:43.111][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-06-29 16:01:43.111][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2024-06-29 16:01:43.111][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2024-06-29 16:01:43.116][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-06-29 16:01:43.117][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-06-29 16:01:43.119][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2024-06-29 16:01:43.120][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-06-29 16:01:43.121][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-06-29 16:01:43.122][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-06-29 16:01:43.140][super$initialize] Initialize connector chebi. biodb.DEBUG[2024-06-29 16:01:43.141][super$initialize] Register connector chebi with the request scheduler biodb.DEBUG[2024-06-29 16:01:43.144][private$bdb$getRequestScheduler()$re ...] Register connector chebi. biodb.DEBUG[2024-06-29 16:01:43.148][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi". biodb.DEBUG[2024-06-29 16:01:43.151][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-06-29 16:01:43.152][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-06-29 16:01:43.153][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk". biodb.DEBUG[2024-06-29 16:01:43.154][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2024-06-29 16:01:43.161][biodb::testThat] biodb.INFO [2024-06-29 16:01:43.162][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-06-29 16:01:43.163][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:01:43.163][biodb::testThat] biodb.TRACE[2024-06-29 16:01:43.166][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-15440-content.xml". biodb.DEBUG[2024-06-29 16:01:43.167][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:43.170][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:43.177][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:43.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.191][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:43.198][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.199][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.200][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.201][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.213][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:43.214][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:43.214][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.215][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.234][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:43.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:43.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.237][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:43.238][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:43.239][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.240][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.240][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:43.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:43.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.244][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.253][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.254][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.254][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.258][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.259][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.260][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.260][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.264][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.265][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.265][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.266][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.267][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.270][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:43.270][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.271][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.272][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.273][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:43.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.275][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.276][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.277][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.278][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.281][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:43.282][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:43.283][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.283][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.284][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:43.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:43.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.287][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:43.288][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:43.289][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.289][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.290][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:43.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:43.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.293][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:43.294][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:43.295][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.295][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.296][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:43.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:43.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:43.352][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440. biodb.TRACE[2024-06-29 16:01:43.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.414][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-29 16:01:43.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-29 16:01:43.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.417][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-29 16:01:43.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-29 16:01:43.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.420][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-29 16:01:43.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-29 16:01:43.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.423][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-29 16:01:43.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-29 16:01:43.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.506][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.507][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.508][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.509][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.533][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.534][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.535][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.535][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:43.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:43.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:43.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:43.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:43.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:43.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.554][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:43.555][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:43.556][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.557][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:43.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:43.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.567][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:43.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:43.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.570][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:43.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:43.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.573][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:43.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:43.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.576][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:43.577][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:43.578][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.579][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.579][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:43.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:43.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.598][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.599][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.599][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.600][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.619][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.620][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.620][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.621][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.632][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:43.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:43.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.635][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:43.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:43.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.638][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:43.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:43.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.641][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:43.642][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:43.647][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.648][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.648][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:43.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:43.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.658][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:43.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:43.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.661][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:43.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:43.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.665][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:43.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:43.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.668][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:43.669][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:43.669][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.670][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.671][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:43.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:43.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.681][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.684][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.687][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.691][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.692][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.692][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.693][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.694][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.705][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:43.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:43.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.708][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:43.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:43.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.711][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:43.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:43.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.714][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:43.715][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:43.716][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.717][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.717][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:43.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:43.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.728][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.737][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.738][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.739][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.740][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.751][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.760][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.761][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.762][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.763][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.774][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.774][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.775][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.776][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.780][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:43.785][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:43.786][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.787][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.791][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:43.792][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:43.792][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.793][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.797][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.798][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.799][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.800][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.805][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.806][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.806][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.807][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.811][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.812][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.813][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.813][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.817][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.818][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.819][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.820][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.824][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.825][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.826][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.826][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.831][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:43.831][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:43.832][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.833][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.837][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:43.838][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:43.839][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.839][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.843][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:43.844][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:43.845][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.846][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.859][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-2528-content.xml". biodb.DEBUG[2024-06-29 16:01:43.885][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:43.886][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:43.887][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:43.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:43.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:43.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:43.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:43.895][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:43.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:43.897][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.898][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.898][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.899][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.920][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:43.921][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:43.922][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.923][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.924][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:43.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:43.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.927][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:43.927][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:43.928][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.929][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.930][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:43.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:43.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.933][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.934][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.934][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.935][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:43.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:43.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.939][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.940][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.940][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.941][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:43.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:43.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.945][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.946][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.947][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.947][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.948][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:43.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.951][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:43.952][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.953][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.954][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.955][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:43.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:43.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.958][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.958][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.959][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.960][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:43.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.964][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:43.965][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:43.965][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.966][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.967][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:43.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:43.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.970][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:43.971][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:43.972][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.973][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.973][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:43.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:43.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.977][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:43.978][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:43.978][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.979][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.980][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:43.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:43.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:43.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:43.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:43.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:43.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:43.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:44.013][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2528. biodb.TRACE[2024-06-29 16:01:44.032][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.041][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.050][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-29 16:01:44.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-29 16:01:44.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.053][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-29 16:01:44.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-29 16:01:44.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.056][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-29 16:01:44.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-29 16:01:44.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.059][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-29 16:01:44.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-29 16:01:44.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.128][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.129][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.130][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.131][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.154][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.155][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.156][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.157][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.167][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.177][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.177][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.178][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.179][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.190][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.193][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.196][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.199][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.200][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.201][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.202][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.202][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.213][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:44.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.222][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:44.223][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.224][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.225][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.226][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:44.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.245][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.246][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.246][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.247][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.266][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.267][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.268][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.269][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.279][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.287][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.290][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.293][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.293][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.294][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.295][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.295][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.305][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.308][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.311][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.314][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.314][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.315][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.316][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.317][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.326][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.329][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.332][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.335][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.336][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.337][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.337][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.338][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.348][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.351][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.354][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.357][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.357][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.358][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.359][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.360][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.378][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.379][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.380][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.380][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.396][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.399][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.400][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.401][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.402][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.403][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.416][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.417][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.418][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.418][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.423][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.423][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.424][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.425][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.429][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.429][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.430][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.431][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.434][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.435][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.436][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.436][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.440][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.441][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.442][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.443][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.447][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.447][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.448][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.449][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.453][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.454][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.454][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.455][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.459][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.460][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.461][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.461][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.466][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.466][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.467][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.468][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.472][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.472][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.473][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.474][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.477][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.478][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.479][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.480][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.484][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-7799-content.xml". biodb.DEBUG[2024-06-29 16:01:44.485][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:44.486][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:44.488][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:44.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:44.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:44.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:44.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:44.495][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:44.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:44.497][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.498][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.498][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.499][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.503][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.504][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.505][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.505][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.506][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.509][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.510][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.511][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.511][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.512][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.515][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.516][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.517][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.517][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.521][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.522][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.522][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.523][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.527][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.528][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.529][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.530][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.531][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.534][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:44.535][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.536][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.537][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.537][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:44.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.540][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.541][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.542][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.546][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.550][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.551][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.552][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.552][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.556][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:44.557][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.557][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.558][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.559][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:44.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.562][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.563][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.563][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.564][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.565][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:44.597][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 7799. biodb.TRACE[2024-06-29 16:01:44.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.602][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.608][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.617][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-29 16:01:44.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-29 16:01:44.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.619][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-29 16:01:44.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-29 16:01:44.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.623][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-29 16:01:44.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-29 16:01:44.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.626][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-29 16:01:44.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-29 16:01:44.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:44.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.688][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.688][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.689][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.690][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.700][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.703][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.706][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.709][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.710][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.710][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.711][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.712][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.728][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.731][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.732][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.732][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.733][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.752][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.753][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.753][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.754][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.765][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.768][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.771][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.774][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.775][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.776][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.776][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.777][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.800][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.801][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.802][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.803][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.821][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.822][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.823][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.823][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.834][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.837][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.840][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.844][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.844][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.845][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.846][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.847][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.857][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.860][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.863][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.866][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.867][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.868][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.868][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.869][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.884][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.887][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.888][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.889][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.889][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.890][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.900][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.903][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.906][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.909][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.910][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.911][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.911][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.912][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.927][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:44.928][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:44.928][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.929][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.933][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:44.934][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:44.934][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.935][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.939][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:44.940][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:44.941][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.941][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.945][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:44.946][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:44.947][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.947][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.951][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:44.952][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:44.953][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.954][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.958][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.959][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:44.959][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.960][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.964][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.965][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:44.966][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.966][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.970][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.971][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:44.972][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.972][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.976][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:01:44.977][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:44.978][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.979][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.983][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:44.984][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:44.985][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.985][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:44.990][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:44.991][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:44.991][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:44.992][ef$get] fields variable is a list. biodb.INFO [2024-06-29 16:01:44.999][biodb::testThat] biodb.INFO [2024-06-29 16:01:45.000][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-06-29 16:01:45.001][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:01:45.001][biodb::testThat] biodb.DEBUG[2024-06-29 16:01:45.003][private$loadEntries] Creating entries from ids [3]: "15440, 2528, 7799". biodb.DEBUG[2024-06-29 16:01:45.008][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)... biodb.TRACE[2024-06-29 16:01:45.011][cch$loadFileContent] Trying to load 3 files from cache: [3]: "15440, 2528, 7799". biodb.TRACE[2024-06-29 16:01:45.014][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, TRUE". biodb.TRACE[2024-06-29 16:01:45.016][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml". biodb.DEBUG[2024-06-29 16:01:45.017][conn$getEntryContent] 2 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:45.017][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:45.018][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:45.019][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:45.022][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:45.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:45.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:45.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:45.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:45.029][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:45.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:45.031][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". biodb.DEBUG[2024-06-29 16:01:45.046][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:45.047][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:45.048][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". biodb.TRACE[2024-06-29 16:01:45.981][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440). biodb.DEBUG[2024-06-29 16:01:46.637][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:46.640][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5c6fb88c946e8568cc03c0d73dc5603e.content" biodb.TRACE[2024-06-29 16:01:46.650][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5c6fb88c946e8568cc03c0d73dc5603e.request" biodb.TRACE[2024-06-29 16:01:46.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml" biodb.DEBUG[2024-06-29 16:01:46.654][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:46.655][self$createEntryFromContent] Creating ChEBI entries from 3 content(s). biodb.DEBUG[2024-06-29 16:01:46.655][self$createEntryFromContent] Parsing 3 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:46.657][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:46.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:46.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:46.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:46.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:46.664][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:46.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:46.666][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.667][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.668][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.669][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.682][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:46.683][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:46.684][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.684][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.685][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:46.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:46.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.688][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:46.689][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:46.690][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.690][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.691][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:46.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:46.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.695][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:46.695][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:46.696][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.697][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:46.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:46.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.701][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:46.701][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:46.702][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.703][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:46.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:46.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.707][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.708][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.709][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.709][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.710][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.714][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:46.714][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:46.715][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.716][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.717][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:46.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:46.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.720][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.720][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.721][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.722][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.726][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:46.727][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:46.727][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.728][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:46.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:46.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.732][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:46.733][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:46.734][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.734][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.735][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:46.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:46.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.738][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:46.739][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:46.740][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.741][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.742][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:46.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:46.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.758][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:46.765][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:46.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:46.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:46.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:46.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:46.776][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:46.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:46.778][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.779][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.780][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.781][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.784][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:46.785][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:46.786][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.787][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.788][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:46.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:46.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.791][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:46.791][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:46.792][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.793][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.794][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:46.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:46.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.797][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:46.798][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:46.799][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.799][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:46.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:46.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.803][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:46.804][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:46.805][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.805][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.806][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:46.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:46.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.809][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.810][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.811][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.811][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.812][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.815][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:46.816][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:46.817][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.818][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.819][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:46.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:46.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.822][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.822][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.823][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.824][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.828][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:46.829][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:46.829][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.830][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.831][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:46.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:46.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.834][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:46.835][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:46.836][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.837][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.838][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:46.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:46.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.841][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:46.842][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:46.842][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.843][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.844][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:46.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:46.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:46.873][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:46.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:46.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:46.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:46.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:46.880][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:46.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:46.883][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.884][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.884][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.885][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.889][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:46.890][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:46.891][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.892][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.893][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:46.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:46.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.896][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:46.896][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:46.897][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.898][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.899][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:46.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:46.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.902][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:46.903][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:46.903][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.904][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:46.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:46.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.908][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:46.909][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:46.910][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.910][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:46.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:46.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.914][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.915][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.916][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.917][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.918][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:46.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.921][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:46.922][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:46.922][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.923][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.924][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:46.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:46.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.927][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.928][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.928][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.929][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:46.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.933][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:46.934][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:46.934][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.935][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:46.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:46.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.939][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:46.940][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:46.940][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.941][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.942][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:46.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:46.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.945][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:46.946][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:46.947][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.947][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.948][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:46.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:46.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:46.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:46.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:46.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:46.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:46.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:47.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:47.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:47.003][self$createEntryFromContent] Accession numbers: 15440, 2528, 7799. biodb.TRACE[2024-06-29 16:01:47.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-06-29 16:01:47.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-06-29 16:01:47.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-06-29 16:01:47.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-06-29 16:01:47.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-06-29 16:01:47.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-06-29 16:01:47.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-06-29 16:01:47.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-06-29 16:01:47.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-06-29 16:01:47.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-06-29 16:01:47.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-06-29 16:01:47.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-06-29 16:01:47.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-06-29 16:01:47.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-06-29 16:01:47.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-06-29 16:01:47.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-06-29 16:01:47.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-06-29 16:01:47.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-06-29 16:01:47.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-29 16:01:47.045][biodb::testThat] biodb.INFO [2024-06-29 16:01:47.046][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-06-29 16:01:47.047][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:01:47.048][biodb::testThat] biodb.TRACE[2024-06-29 16:01:47.050][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:47.051][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:47.051][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.052][ef$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:47.053][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name". biodb.TRACE[2024-06-29 16:01:47.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:47.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:47.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.081][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:47.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:47.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:47.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:47.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:47.089][function(conn, opt)] With value "squalene". biodb.DEBUG[2024-06-29 16:01:47.105][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". biodb.DEBUG[2024-06-29 16:01:47.108][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:01:47.119][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05". biodb.TRACE[2024-06-29 16:01:47.120][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:01:47.122][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content". biodb.DEBUG[2024-06-29 16:01:47.124][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:01:47.127][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:01:47.128][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-06-29 16:01:47.129][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:01:47.131][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-06-29 16:01:47.132][function(conn, opt)] With found IDs [1]: "15440". biodb.TRACE[2024-06-29 16:01:47.143][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:47.144][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:47.145][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.146][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.146][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:47.147][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:47.148][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.149][ef$get] fields variable is a list. biodb.INFO [2024-06-29 16:01:47.152][biodb::testThat] biodb.INFO [2024-06-29 16:01:47.153][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-06-29 16:01:47.154][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:01:47.155][biodb::testThat] biodb.TRACE[2024-06-29 16:01:47.179][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:47.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:47.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:47.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:47.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.186][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:47.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:47.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:47.230][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:01:47.233][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:01:47.234][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-06-29 16:01:47.235][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:01:47.236][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.INFO [2024-06-29 16:01:47.251][biodb::testThat] biodb.INFO [2024-06-29 16:01:47.252][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-06-29 16:01:47.253][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:01:47.253][biodb::testThat] biodb.TRACE[2024-06-29 16:01:47.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:47.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:47.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:47.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:47.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:47.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:47.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.275][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:47.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:47.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:47.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:47.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:47.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:47.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.285][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-29 16:01:47.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-29 16:01:47.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.288][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-29 16:01:47.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-29 16:01:47.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.291][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-29 16:01:47.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-29 16:01:47.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.294][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-29 16:01:47.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-29 16:01:47.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.304][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:47.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:47.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:47.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:47.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.310][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:47.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:47.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.313][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:47.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:47.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:47.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:47.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:47.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:47.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.322][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-29 16:01:47.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-29 16:01:47.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.325][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-29 16:01:47.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-29 16:01:47.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.328][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-29 16:01:47.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-29 16:01:47.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:47.331][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-29 16:01:47.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-29 16:01:47.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:47.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-29 16:01:47.339][biodb::testThat] biodb.INFO [2024-06-29 16:01:47.340][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-06-29 16:01:47.341][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:01:47.341][biodb::testThat] biodb.INFO [2024-06-29 16:01:47.349][biodb::testThat] biodb.INFO [2024-06-29 16:01:47.350][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-06-29 16:01:47.351][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:01:47.352][biodb::testThat] biodb.INFO [2024-06-29 16:01:47.378][biodb::testThat] biodb.INFO [2024-06-29 16:01:47.379][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-06-29 16:01:47.379][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:01:47.380][biodb::testThat] biodb.DEBUG[2024-06-29 16:01:47.383][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440". biodb.DEBUG[2024-06-29 16:01:48.087][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440. biodb.INFO [2024-06-29 16:01:49.110][biodb::testThat] biodb.INFO [2024-06-29 16:01:49.111][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-06-29 16:01:49.111][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:01:49.112][biodb::testThat] biodb.DEBUG[2024-06-29 16:01:49.481][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400. biodb.TRACE[2024-06-29 16:01:49.848][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:49.849][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:49.850][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:49.850][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:49.851][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:49.852][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:49.852][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:49.853][ef$get] fields variable is a list. biodb.INFO [2024-06-29 16:01:49.855][biodb::testThat] biodb.INFO [2024-06-29 16:01:49.855][biodb::testThat] Running test function test.searchCompound (" We can search for a compound "). biodb.INFO [2024-06-29 16:01:49.856][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:01:49.857][biodb::testThat] biodb.TRACE[2024-06-29 16:01:49.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:49.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:49.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:49.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:49.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:49.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:49.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:49.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:49.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:49.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:49.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:49.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:49.943][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:01:49.946][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:01:49.947][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-06-29 16:01:49.948][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:01:49.949][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-06-29 16:01:49.994][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:01:49.996][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:01:49.997][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-06-29 16:01:49.998][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:01:49.999][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.TRACE[2024-06-29 16:01:50.016][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:01:50.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:01:50.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:50.042][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:01:50.045][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:01:50.046][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-06-29 16:01:50.046][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:01:50.048][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-06-29 16:01:50.050][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:50.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:50.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:50.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:50.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:50.057][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:50.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:50.058][private$loadEntries] Creating entries from ids [1]: "192288". biodb.DEBUG[2024-06-29 16:01:50.096][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:50.097][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288". biodb.TRACE[2024-06-29 16:01:50.098][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:50.099][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:50.099][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:50.100][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:50.101][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:50.102][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:50.111][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:50.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:50.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:50.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:50.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:50.118][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:50.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:50.120][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288". biodb.DEBUG[2024-06-29 16:01:50.130][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:50.131][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:50.142][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288". biodb.TRACE[2024-06-29 16:01:50.484][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288). biodb.DEBUG[2024-06-29 16:01:50.820][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:50.821][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content" biodb.TRACE[2024-06-29 16:01:50.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request" biodb.TRACE[2024-06-29 16:01:50.826][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml" biodb.DEBUG[2024-06-29 16:01:50.828][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:50.829][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:50.830][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:50.831][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:50.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:50.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:50.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:50.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:50.838][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:50.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:50.847][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:50.848][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:50.848][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.849][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:50.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:50.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.853][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:50.854][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:50.854][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.855][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.856][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:50.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:50.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.859][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:50.859][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:50.860][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.861][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.862][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:50.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:50.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.865][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:50.866][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:50.866][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.867][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:50.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:50.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.871][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:50.872][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:50.872][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.873][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:50.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:50.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.877][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:50.878][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:50.878][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.879][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.880][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:50.881][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.882][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.882][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.883][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:50.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.886][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:50.887][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:50.888][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.888][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:50.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:50.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.892][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:50.893][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:50.894][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.894][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:50.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:50.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.899][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:50.899][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:50.900][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.901][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.902][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:50.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:50.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.905][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:50.906][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:50.907][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.907][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.908][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:50.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:50.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:50.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:50.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:50.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:50.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:50.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:50.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:50.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:50.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:50.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:50.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:50.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:50.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:50.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:50.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:50.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:50.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:50.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:50.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:50.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:50.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:50.946][self$createEntryFromContent] Accession numbers: 192288. biodb.TRACE[2024-06-29 16:01:50.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:50.962][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:01:50.965][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:01:50.966][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-06-29 16:01:50.967][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:01:50.968][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-06-29 16:01:50.979][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:50.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:50.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:50.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:50.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:50.986][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:50.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:50.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:50.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:50.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:50.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:50.996][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:50.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:50.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:51.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:51.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:51.004][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:51.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:51.005][private$loadEntries] Creating entries from ids [1]: "209892". biodb.DEBUG[2024-06-29 16:01:51.006][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:51.007][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892". biodb.TRACE[2024-06-29 16:01:51.008][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:51.009][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:51.010][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:51.011][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:51.016][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:51.017][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:51.019][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:51.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:51.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:51.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:51.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:51.026][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:51.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:51.028][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892". biodb.DEBUG[2024-06-29 16:01:51.030][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:51.031][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:51.032][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892". biodb.TRACE[2024-06-29 16:01:51.373][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892). biodb.DEBUG[2024-06-29 16:01:51.709][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:51.710][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content" biodb.TRACE[2024-06-29 16:01:51.713][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request" biodb.TRACE[2024-06-29 16:01:51.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml" biodb.DEBUG[2024-06-29 16:01:51.716][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:51.717][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:51.718][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:51.719][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:51.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:51.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:51.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:51.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:51.726][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:51.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:51.728][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:51.729][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:51.730][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.731][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:51.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:51.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.734][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:51.735][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:51.736][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.737][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.738][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:51.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:51.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.741][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:51.741][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:51.742][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.743][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.744][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:51.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:51.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.747][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:51.748][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:51.748][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.749][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:51.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:51.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.753][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:51.754][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:51.755][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.756][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:51.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:51.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.760][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:51.761][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:51.761][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.762][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.763][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:51.764][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.765][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.766][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.766][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:51.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.770][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:51.770][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:51.771][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.772][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:51.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:51.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.776][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:51.777][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:51.778][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.785][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:51.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:51.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.789][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:51.789][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:51.790][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.791][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.792][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:51.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:51.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.795][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:51.796][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:51.797][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.797][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.798][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:51.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:51.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:51.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:51.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:51.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:51.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:51.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:51.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:51.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:51.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:51.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:51.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:51.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:51.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:51.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:51.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:51.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:51.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:51.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:51.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:51.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:51.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:51.831][self$createEntryFromContent] Accession numbers: 209892. biodb.TRACE[2024-06-29 16:01:51.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:51.857][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:01:51.860][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:01:51.861][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-06-29 16:01:51.862][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:01:51.863][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-06-29 16:01:51.865][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:51.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:51.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:51.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:51.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:51.872][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:51.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:51.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:51.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:51.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:51.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:51.887][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:51.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:51.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:51.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:51.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:51.894][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:51.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:51.896][private$loadEntries] Creating entries from ids [1]: "26747". biodb.DEBUG[2024-06-29 16:01:51.897][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:51.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747". biodb.TRACE[2024-06-29 16:01:51.899][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:51.900][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:51.901][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:51.902][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:51.903][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:51.903][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:51.906][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:51.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:51.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:51.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:51.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:51.913][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:51.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:51.915][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747". biodb.DEBUG[2024-06-29 16:01:51.917][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:51.918][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:51.919][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747". biodb.TRACE[2024-06-29 16:01:52.259][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747). biodb.DEBUG[2024-06-29 16:01:52.597][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:52.599][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content" biodb.TRACE[2024-06-29 16:01:52.601][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request" biodb.TRACE[2024-06-29 16:01:52.603][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml" biodb.DEBUG[2024-06-29 16:01:52.605][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:52.606][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:52.607][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:52.608][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:52.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:52.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:52.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:52.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:52.615][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:52.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:52.618][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:52.619][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:52.620][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.621][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:52.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:52.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.625][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:52.626][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:52.626][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.627][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.628][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:52.629][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:52.630][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.631][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.632][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:52.633][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:52.633][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.634][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.635][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:52.636][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:52.637][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.637][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.638][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:52.639][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:52.640][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.640][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.641][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:52.642][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:52.643][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.644][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.645][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:52.652][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:52.653][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.654][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.655][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:52.656][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:52.656][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.657][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:52.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:52.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.661][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:52.661][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:52.662][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.663][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.664][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:52.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:52.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.667][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:52.668][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:52.668][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.669][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:52.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:52.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:52.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:52.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:52.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:52.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:52.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:52.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:52.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:52.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:52.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:52.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:52.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:52.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:52.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:52.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:52.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:52.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:52.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:52.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:52.701][self$createEntryFromContent] Accession numbers: 26747. biodb.TRACE[2024-06-29 16:01:52.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:52.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:52.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:52.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:52.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:52.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:52.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:52.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:52.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:52.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:52.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:52.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:52.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:52.717][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:52.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:52.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:52.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:52.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:52.724][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:52.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:52.725][private$loadEntries] Creating entries from ids [1]: "59285". biodb.DEBUG[2024-06-29 16:01:52.726][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:52.727][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285". biodb.TRACE[2024-06-29 16:01:52.728][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:52.729][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:52.730][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:52.731][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:52.732][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:52.733][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:52.735][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:52.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:52.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:52.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:52.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:52.746][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:52.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:52.748][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285". biodb.DEBUG[2024-06-29 16:01:52.750][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:52.751][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:52.752][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285". biodb.TRACE[2024-06-29 16:01:53.097][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285). biodb.DEBUG[2024-06-29 16:01:53.431][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:53.433][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content" biodb.TRACE[2024-06-29 16:01:53.436][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request" biodb.TRACE[2024-06-29 16:01:53.438][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml" biodb.DEBUG[2024-06-29 16:01:53.439][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:53.440][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:53.441][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:53.443][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:53.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:53.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:53.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:53.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:53.450][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:53.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:53.452][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:53.453][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:53.454][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.455][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:53.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:53.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.459][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:53.459][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:53.460][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.461][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.462][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:53.463][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:53.463][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.464][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.465][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:53.466][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:53.467][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.468][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.469][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:53.469][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:53.470][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.471][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.472][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:53.473][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:53.473][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.474][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.475][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:53.476][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:53.477][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.477][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.478][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:53.479][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:53.480][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.481][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.481][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:53.482][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:53.483][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.484][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:53.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:53.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.488][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:53.489][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:53.489][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.490][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.491][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:53.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:53.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.494][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:53.495][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:53.496][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.496][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:53.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:53.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:53.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:53.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:53.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:53.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:53.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:53.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:53.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:53.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:53.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:53.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:53.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:53.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:53.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:53.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:53.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:53.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:53.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:53.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:53.535][self$createEntryFromContent] Accession numbers: 59285. biodb.TRACE[2024-06-29 16:01:53.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:53.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:53.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:53.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:53.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:53.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:53.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:53.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:53.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:53.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:53.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:53.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:53.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:53.551][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:53.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:53.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:53.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:53.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:53.558][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:53.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:53.559][private$loadEntries] Creating entries from ids [1]: "75174". biodb.DEBUG[2024-06-29 16:01:53.560][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:53.561][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174". biodb.TRACE[2024-06-29 16:01:53.562][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:53.563][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:53.564][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:53.565][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:53.566][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:53.566][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:53.568][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:53.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:53.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:53.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:53.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:53.575][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:53.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:53.577][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174". biodb.DEBUG[2024-06-29 16:01:53.579][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:53.580][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:53.581][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174". biodb.TRACE[2024-06-29 16:01:53.922][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174). biodb.DEBUG[2024-06-29 16:01:54.260][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:54.262][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content" biodb.TRACE[2024-06-29 16:01:54.265][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request" biodb.TRACE[2024-06-29 16:01:54.267][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml" biodb.DEBUG[2024-06-29 16:01:54.268][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:54.269][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:54.270][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:54.271][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:54.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:54.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:54.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:54.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:54.285][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:54.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:54.288][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:54.289][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:54.289][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.290][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:54.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:54.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.295][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:54.295][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:54.296][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.297][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.298][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:54.299][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:54.300][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.300][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.301][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:54.302][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:54.303][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.304][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.305][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:54.306][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:54.306][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.307][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.308][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:54.309][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:54.310][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.310][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.311][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:54.312][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:54.313][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.313][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.314][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:54.315][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:54.316][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.317][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.318][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:54.318][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:54.319][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.320][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:54.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:54.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.324][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:54.325][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:54.326][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.327][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.328][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:54.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:54.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.330][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:54.331][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:54.332][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.333][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:54.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:54.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:54.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:54.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:54.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:54.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:54.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:54.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:54.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:54.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:54.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:54.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:54.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:54.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:54.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:54.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:54.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:54.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:54.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:54.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:54.366][self$createEntryFromContent] Accession numbers: 75174. biodb.TRACE[2024-06-29 16:01:54.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:54.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:54.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:54.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:54.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:54.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:54.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:54.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:54.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:54.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:54.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:54.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:54.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:54.386][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:54.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:54.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:54.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:54.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:54.394][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:54.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:54.395][private$loadEntries] Creating entries from ids [1]: "15441". biodb.DEBUG[2024-06-29 16:01:54.396][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:54.397][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441". biodb.TRACE[2024-06-29 16:01:54.398][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:54.399][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:54.400][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:54.401][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:54.402][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:54.402][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:54.405][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:54.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:54.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:54.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:54.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:54.412][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:54.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:54.414][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441". biodb.DEBUG[2024-06-29 16:01:54.416][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:54.417][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:54.418][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441". biodb.TRACE[2024-06-29 16:01:54.768][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441). biodb.DEBUG[2024-06-29 16:01:55.108][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:55.110][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content" biodb.TRACE[2024-06-29 16:01:55.113][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request" biodb.TRACE[2024-06-29 16:01:55.115][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml" biodb.DEBUG[2024-06-29 16:01:55.117][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:55.118][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:55.119][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:55.120][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:55.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:55.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:55.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:55.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:55.127][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:55.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:55.130][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:55.131][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:55.132][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.132][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:55.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:55.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.137][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:55.138][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:55.138][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.139][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.140][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:55.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:55.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.144][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:55.145][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:55.145][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.146][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.147][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:55.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:55.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.151][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:55.152][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:55.153][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.153][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.161][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:55.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:55.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.165][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:55.166][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:55.167][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.167][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:55.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:55.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.171][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:55.172][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:55.173][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.174][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.175][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:55.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:55.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.178][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:55.179][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:55.180][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.181][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.182][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:55.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:55.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.186][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:55.187][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:55.188][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.189][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:55.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:55.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.193][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:55.194][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:55.195][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.196][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:55.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:55.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.201][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:55.202][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:55.203][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.203][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.204][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:55.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:55.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.208][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:55.209][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:55.209][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.210][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.211][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:55.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:55.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:55.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:55.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:55.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:55.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:55.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:55.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:55.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:55.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:55.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:55.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:55.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:55.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:55.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:55.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:55.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:55.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:55.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:55.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:55.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:55.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:55.250][self$createEntryFromContent] Accession numbers: 15441. biodb.TRACE[2024-06-29 16:01:55.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:55.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:55.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:55.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:55.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:55.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:55.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:55.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:55.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:55.266][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:55.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:55.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:55.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:55.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:55.273][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:55.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:55.274][private$loadEntries] Creating entries from ids [1]: "15442". biodb.DEBUG[2024-06-29 16:01:55.275][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:55.276][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442". biodb.TRACE[2024-06-29 16:01:55.277][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:55.278][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:55.279][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:55.280][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:55.281][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:55.281][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:55.283][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:55.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:55.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:55.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:55.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:55.291][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:55.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:55.292][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442". biodb.DEBUG[2024-06-29 16:01:55.295][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:55.295][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:55.296][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442". biodb.TRACE[2024-06-29 16:01:55.657][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442). biodb.DEBUG[2024-06-29 16:01:55.993][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:55.995][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content" biodb.TRACE[2024-06-29 16:01:55.998][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request" biodb.TRACE[2024-06-29 16:01:56.000][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml" biodb.DEBUG[2024-06-29 16:01:56.001][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:56.002][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:56.003][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:56.004][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:56.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:56.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:56.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:56.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:56.011][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:56.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:56.014][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.015][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.016][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.016][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.021][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:56.022][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:56.023][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.023][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.024][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:56.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:56.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.028][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:56.029][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:56.029][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.030][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.031][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:56.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:56.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.034][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:56.035][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:56.036][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.037][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:56.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:56.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.041][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:56.042][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:56.043][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.044][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:56.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:56.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.055][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:56.056][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:56.056][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.057][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.058][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:56.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:56.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.061][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:56.062][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:56.063][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.064][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.065][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:56.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:56.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.068][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:56.068][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:56.069][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.070][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:56.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:56.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.074][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:56.075][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:56.075][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.076][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.077][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:56.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:56.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.080][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:56.081][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:56.082][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.083][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.084][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:56.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:56.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.087][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:56.088][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:56.089][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.089][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.090][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:56.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:56.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:56.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:56.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:56.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:56.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:56.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:56.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:56.124][self$createEntryFromContent] Accession numbers: 15442. biodb.TRACE[2024-06-29 16:01:56.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:56.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:56.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:56.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:56.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:56.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:56.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:56.134][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:56.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:56.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:56.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:56.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:56.146][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:56.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:56.147][private$loadEntries] Creating entries from ids [1]: "57310". biodb.DEBUG[2024-06-29 16:01:56.148][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:56.149][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310". biodb.TRACE[2024-06-29 16:01:56.150][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:56.151][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:56.152][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:56.152][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:56.153][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:56.154][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:56.156][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:56.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:56.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:56.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:56.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:56.163][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:56.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:56.165][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310". biodb.DEBUG[2024-06-29 16:01:56.167][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:56.168][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:56.169][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310". biodb.TRACE[2024-06-29 16:01:56.513][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310). biodb.DEBUG[2024-06-29 16:01:56.896][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:56.898][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content" biodb.TRACE[2024-06-29 16:01:56.901][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request" biodb.TRACE[2024-06-29 16:01:56.903][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml" biodb.DEBUG[2024-06-29 16:01:56.904][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:56.905][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:56.906][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:56.907][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:56.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:56.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:56.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:56.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:56.914][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:56.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:56.917][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.918][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.919][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.919][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.924][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:56.924][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:56.925][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.926][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.927][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:56.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:56.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.930][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:56.931][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:56.932][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.933][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.934][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:56.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:56.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.937][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:56.937][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:56.938][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.939][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:56.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:56.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.943][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:56.944][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:56.945][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.945][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.946][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:56.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:56.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.949][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:56.950][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:56.951][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.952][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.953][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:56.960][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:56.961][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.962][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.963][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:56.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:56.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.966][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:56.967][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:56.968][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.968][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:56.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:56.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.972][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:56.973][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:56.974][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.974][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:56.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:56.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.978][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:56.979][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:56.980][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.980][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.981][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:56.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:56.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.984][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:56.985][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:56.986][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.987][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.988][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:56.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:56.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:56.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:56.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:56.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:56.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:56.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:56.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:56.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:56.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:57.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:57.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:57.021][self$createEntryFromContent] Accession numbers: 57310. biodb.TRACE[2024-06-29 16:01:57.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:57.031][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:57.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:57.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:57.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:57.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:57.038][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:57.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:57.040][private$loadEntries] Creating entries from ids [1]: "66216". biodb.DEBUG[2024-06-29 16:01:57.040][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:57.042][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216". biodb.TRACE[2024-06-29 16:01:57.047][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:57.048][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:57.048][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:57.049][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:57.050][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:57.051][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:57.052][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:57.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:57.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:57.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:57.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:57.059][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:57.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:57.061][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216". biodb.DEBUG[2024-06-29 16:01:57.063][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:57.064][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:57.065][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216". biodb.TRACE[2024-06-29 16:01:57.406][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216). biodb.DEBUG[2024-06-29 16:01:57.738][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:57.740][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content" biodb.TRACE[2024-06-29 16:01:57.743][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request" biodb.TRACE[2024-06-29 16:01:57.745][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml" biodb.DEBUG[2024-06-29 16:01:57.747][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:57.748][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:57.749][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:57.750][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:57.751][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:57.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:57.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:57.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:57.757][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:57.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:57.760][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.760][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.761][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.762][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.766][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:57.767][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:57.768][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.769][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.770][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:57.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:57.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.773][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:57.774][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:57.775][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.776][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.777][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:57.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:57.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.780][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:57.781][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:57.781][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.782][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:57.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:57.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.786][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:57.787][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:57.788][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.789][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:57.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:57.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.793][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:57.794][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:57.794][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.795][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.796][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:57.797][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.798][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.799][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.800][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:57.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.803][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:57.804][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:57.805][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.805][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:57.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:57.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.817][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:57.818][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:57.818][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.819][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:57.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:57.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.824][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:57.825][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:57.826][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.827][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.828][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:57.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:57.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.831][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:57.832][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:57.832][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.833][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.834][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:57.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:57.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:57.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:57.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:57.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:57.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:57.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:57.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:57.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:57.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:57.869][self$createEntryFromContent] Accession numbers: 66216. biodb.TRACE[2024-06-29 16:01:57.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:57.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:57.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:57.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:57.879][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:57.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:57.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:57.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:57.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:57.887][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:57.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:57.889][private$loadEntries] Creating entries from ids [1]: "70860". biodb.DEBUG[2024-06-29 16:01:57.890][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:57.891][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860". biodb.TRACE[2024-06-29 16:01:57.892][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:57.893][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:57.894][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:57.895][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:57.895][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:57.896][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:57.898][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:57.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:57.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:57.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:57.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:57.916][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:57.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:57.918][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860". biodb.DEBUG[2024-06-29 16:01:57.920][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:57.921][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:57.922][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860". biodb.TRACE[2024-06-29 16:01:58.261][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860). biodb.DEBUG[2024-06-29 16:01:58.606][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:58.608][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content" biodb.TRACE[2024-06-29 16:01:58.611][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request" biodb.TRACE[2024-06-29 16:01:58.613][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml" biodb.DEBUG[2024-06-29 16:01:58.614][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:58.615][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:58.617][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:58.618][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:58.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:58.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:58.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:58.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:58.625][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:58.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:58.628][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:58.628][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:58.629][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.630][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:58.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:58.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.634][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:58.635][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:58.636][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.637][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.638][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:58.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:58.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.641][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:58.642][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:58.642][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.643][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.644][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:58.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:58.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.648][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:58.649][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:58.649][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.650][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:58.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:58.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.654][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:58.655][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:58.656][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.657][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:58.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:58.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.661][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:58.661][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:58.662][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.663][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.664][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:58.665][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:58.666][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.666][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.667][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:58.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:58.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.671][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:58.672][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:58.672][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.673][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:58.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:58.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.677][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:58.678][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:58.679][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.680][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:58.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:58.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.684][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:58.689][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:58.692][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.693][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.694][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:58.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:58.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.698][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:58.698][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:58.699][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.700][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.701][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:58.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:58.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:58.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:58.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:58.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:58.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:58.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:58.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:58.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:58.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:58.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:58.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:58.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:58.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:58.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:58.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:58.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:58.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:58.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:58.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:58.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:58.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:58.736][self$createEntryFromContent] Accession numbers: 70860. biodb.TRACE[2024-06-29 16:01:58.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:58.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:58.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:58.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:58.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:58.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:58.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:58.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:58.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:58.746][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:58.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:58.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:58.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:58.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:58.753][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:58.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:58.754][private$loadEntries] Creating entries from ids [1]: "70861". biodb.DEBUG[2024-06-29 16:01:58.755][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:58.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861". biodb.TRACE[2024-06-29 16:01:58.757][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:58.758][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:58.759][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:58.760][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:58.761][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:58.761][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:58.763][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:58.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:58.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:58.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:58.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:58.771][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:58.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:58.773][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861". biodb.DEBUG[2024-06-29 16:01:58.775][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:58.775][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:58.777][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861". biodb.TRACE[2024-06-29 16:01:59.125][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861). biodb.DEBUG[2024-06-29 16:01:59.491][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:01:59.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content" biodb.TRACE[2024-06-29 16:01:59.502][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request" biodb.TRACE[2024-06-29 16:01:59.505][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml" biodb.DEBUG[2024-06-29 16:01:59.506][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:01:59.507][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:01:59.508][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:01:59.509][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:59.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:59.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:59.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:59.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:59.516][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:59.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:01:59.518][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:59.519][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:59.520][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.520][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:59.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:59.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.524][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:59.525][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:59.526][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.527][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.528][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:01:59.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:01:59.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.531][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:59.531][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:59.532][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.533][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.534][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:01:59.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:01:59.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.537][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:59.538][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:59.539][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.539][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:01:59.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:01:59.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.544][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:59.544][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:59.545][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.546][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:01:59.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:01:59.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.550][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:59.551][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:01:59.552][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.552][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.553][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:59.554][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:59.555][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.556][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.557][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:01:59.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:59.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.560][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:59.561][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:59.561][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.562][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:59.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:01:59.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.566][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:59.567][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:59.567][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.568][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:01:59.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:01:59.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.572][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:59.573][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:59.574][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.574][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.575][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:01:59.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:01:59.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.579][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:59.580][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:59.580][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.581][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.582][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:01:59.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:01:59.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:59.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:59.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:59.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:59.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:59.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:59.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:01:59.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:01:59.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:59.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:59.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:59.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:59.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:59.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:59.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:59.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:59.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:59.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:59.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:01:59.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:01:59.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:59.621][self$createEntryFromContent] Accession numbers: 70861. biodb.TRACE[2024-06-29 16:01:59.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:59.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:59.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:59.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:59.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:01:59.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:01:59.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:01:59.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:01:59.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:01:59.632][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:59.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:59.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:59.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:59.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:59.639][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:59.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:59.641][private$loadEntries] Creating entries from ids [1]: "78662". biodb.DEBUG[2024-06-29 16:01:59.641][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:01:59.643][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662". biodb.TRACE[2024-06-29 16:01:59.644][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:01:59.645][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:01:59.646][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:01:59.646][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:01:59.647][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:01:59.648][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:01:59.650][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:01:59.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:01:59.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:01:59.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:01:59.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:01:59.657][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:01:59.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:01:59.659][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662". biodb.DEBUG[2024-06-29 16:01:59.661][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:01:59.662][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:01:59.663][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662". biodb.TRACE[2024-06-29 16:02:00.006][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662). biodb.DEBUG[2024-06-29 16:02:00.346][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:00.348][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content" biodb.TRACE[2024-06-29 16:02:00.351][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request" biodb.TRACE[2024-06-29 16:02:00.354][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml" biodb.DEBUG[2024-06-29 16:02:00.355][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:00.356][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:00.357][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:00.358][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:00.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:00.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:00.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:00.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:00.373][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:00.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:00.375][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:00.376][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:00.377][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.378][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:00.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:00.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.382][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:00.382][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:00.383][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.384][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.385][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:00.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:00.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.388][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:00.389][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:00.390][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.391][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:00.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:00.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.395][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:00.396][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:00.397][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.397][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.398][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:00.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:00.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.401][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:00.402][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:00.403][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.403][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:00.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:00.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.408][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:00.409][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:00.409][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.410][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.411][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:00.412][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:00.412][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.413][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.414][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:00.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:00.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.417][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:00.418][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:00.419][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.419][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:00.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:00.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.424][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:00.424][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:00.425][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.426][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:00.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:00.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.430][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:00.431][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:00.432][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.433][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.434][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:00.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:00.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.437][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:00.438][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:00.438][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.439][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.440][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:00.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:00.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:00.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:00.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:00.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:00.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:00.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:00.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:00.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:00.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:00.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:00.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:00.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:00.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:00.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:00.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:00.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:00.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:00.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:00.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:00.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:00.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:00.481][self$createEntryFromContent] Accession numbers: 78662. biodb.TRACE[2024-06-29 16:02:00.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:00.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:00.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:00.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:00.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:00.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:00.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:00.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:00.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:00.491][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:00.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:00.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:00.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:00.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:00.498][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:00.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:00.500][private$loadEntries] Creating entries from ids [1]: "85084". biodb.DEBUG[2024-06-29 16:02:00.501][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:00.502][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084". biodb.TRACE[2024-06-29 16:02:00.503][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:00.504][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:00.505][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:00.506][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:00.507][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:00.507][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:00.509][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:00.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:00.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:00.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:00.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:00.517][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:00.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:00.519][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084". biodb.DEBUG[2024-06-29 16:02:00.521][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:00.522][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:00.523][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084". biodb.TRACE[2024-06-29 16:02:00.894][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084). biodb.DEBUG[2024-06-29 16:02:01.237][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:01.239][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content" biodb.TRACE[2024-06-29 16:02:01.242][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request" biodb.TRACE[2024-06-29 16:02:01.244][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml" biodb.DEBUG[2024-06-29 16:02:01.245][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:01.246][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:01.247][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:01.248][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:01.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:01.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:01.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:01.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:01.256][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:01.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:01.259][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:01.260][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:01.260][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.261][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:01.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:01.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.272][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:01.273][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:01.274][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.275][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.276][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:01.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:01.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.279][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:01.280][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:01.281][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.282][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.283][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:01.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:01.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.286][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:01.287][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:01.287][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.288][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.289][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:01.290][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:01.291][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.291][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.292][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:01.293][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:01.294][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.294][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.296][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:01.296][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:01.297][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.298][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.299][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:01.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:01.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.302][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:01.303][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:01.303][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.304][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:01.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:01.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.308][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:01.309][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:01.310][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.310][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:01.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:01.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.314][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:01.315][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:01.316][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.317][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.318][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:01.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:01.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.321][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:01.321][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:01.322][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.323][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:01.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:01.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:01.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:01.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:01.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:01.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:01.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:01.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:01.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:01.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:01.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:01.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:01.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:01.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:01.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:01.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:01.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:01.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:01.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:01.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:01.359][self$createEntryFromContent] Accession numbers: 85084. biodb.TRACE[2024-06-29 16:02:01.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:01.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:01.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:01.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:01.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:01.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:01.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:01.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:01.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:01.369][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:01.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:01.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:01.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:01.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:01.377][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:01.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:01.378][private$loadEntries] Creating entries from ids [1]: "85086". biodb.DEBUG[2024-06-29 16:02:01.379][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:01.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086". biodb.TRACE[2024-06-29 16:02:01.381][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:01.382][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:01.383][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:01.384][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:01.385][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:01.385][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:01.388][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:01.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:01.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:01.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:01.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:01.395][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:01.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:01.397][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086". biodb.DEBUG[2024-06-29 16:02:01.399][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:01.400][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:01.401][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086". biodb.TRACE[2024-06-29 16:02:01.741][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086). biodb.DEBUG[2024-06-29 16:02:02.091][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:02.093][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content" biodb.TRACE[2024-06-29 16:02:02.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request" biodb.TRACE[2024-06-29 16:02:02.097][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml" biodb.DEBUG[2024-06-29 16:02:02.099][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:02.099][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:02.100][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:02.102][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:02.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:02.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:02.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:02.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:02.109][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:02.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:02.111][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:02.112][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:02.113][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.114][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:02.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:02.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.118][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:02.119][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:02.119][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.120][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.121][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:02.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:02.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.124][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:02.125][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:02.125][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.126][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.127][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:02.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:02.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.130][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:02.131][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:02.131][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.132][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.133][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:02.134][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:02.135][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.136][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.144][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:02.145][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:02.146][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.146][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.147][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:02.148][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:02.149][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.150][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.151][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:02.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:02.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.154][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:02.155][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:02.155][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.156][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:02.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:02.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.160][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:02.161][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:02.162][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.163][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:02.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:02.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.167][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:02.168][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:02.169][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.170][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.171][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:02.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:02.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.174][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:02.175][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:02.175][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.176][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:02.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:02.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:02.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:02.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:02.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:02.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:02.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:02.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:02.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:02.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:02.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:02.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:02.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:02.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:02.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:02.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:02.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:02.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:02.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:02.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:02.209][self$createEntryFromContent] Accession numbers: 85086. biodb.TRACE[2024-06-29 16:02:02.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:02.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:02.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:02.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:02.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:02.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:02.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:02.219][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:02.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:02.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:02.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:02.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:02.227][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:02.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:02.228][private$loadEntries] Creating entries from ids [1]: "88123". biodb.DEBUG[2024-06-29 16:02:02.229][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:02.235][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123". biodb.TRACE[2024-06-29 16:02:02.236][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:02.237][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:02.238][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:02.239][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:02.240][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:02.240][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:02.243][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:02.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:02.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:02.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:02.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:02.250][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:02.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:02.252][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123". biodb.DEBUG[2024-06-29 16:02:02.254][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:02.255][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:02.256][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123". biodb.TRACE[2024-06-29 16:02:02.605][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123). biodb.DEBUG[2024-06-29 16:02:02.945][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:02.946][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content" biodb.TRACE[2024-06-29 16:02:02.949][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request" biodb.TRACE[2024-06-29 16:02:02.951][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml" biodb.DEBUG[2024-06-29 16:02:02.953][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:02.954][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:02.955][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:02.956][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:02.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:02.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:02.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:02.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:02.963][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:02.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:02.966][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:02.967][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:02.967][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.968][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:02.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:02.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.972][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:02.973][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:02.974][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.975][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.976][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:02.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:02.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.979][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:02.980][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:02.981][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.982][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.983][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:02.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:02.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.986][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:02.987][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:02.988][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.989][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:02.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:02.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.993][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:02.994][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:02.994][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.995][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:02.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:02.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:02.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:02.999][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:03.000][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:03.001][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.002][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.003][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:03.004][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.004][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.005][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.006][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:03.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.010][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:03.011][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:03.011][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.012][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:03.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:03.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.024][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:03.024][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:03.025][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.026][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:03.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:03.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.030][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:03.031][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:03.031][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.032][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.033][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:03.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:03.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.036][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:03.037][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:03.038][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.038][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.039][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:03.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:03.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:03.074][self$createEntryFromContent] Accession numbers: 88123. biodb.TRACE[2024-06-29 16:02:03.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:03.084][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:03.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:03.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:03.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:03.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:03.091][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:03.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:03.092][private$loadEntries] Creating entries from ids [1]: "134117". biodb.DEBUG[2024-06-29 16:02:03.093][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:03.094][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117". biodb.TRACE[2024-06-29 16:02:03.095][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:03.096][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:03.097][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:03.098][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:03.099][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:03.100][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:03.102][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:03.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:03.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:03.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:03.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:03.114][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:03.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:03.116][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117". biodb.DEBUG[2024-06-29 16:02:03.118][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:03.118][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:03.119][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117". biodb.TRACE[2024-06-29 16:02:03.473][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117). biodb.DEBUG[2024-06-29 16:02:03.812][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:03.813][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content" biodb.TRACE[2024-06-29 16:02:03.816][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request" biodb.TRACE[2024-06-29 16:02:03.818][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml" biodb.DEBUG[2024-06-29 16:02:03.820][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:03.820][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:03.821][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:03.822][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:03.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:03.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:03.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:03.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:03.830][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:03.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:03.832][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.833][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.834][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.835][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.839][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:03.840][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:03.841][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.841][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.842][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:03.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:03.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.845][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:03.846][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:03.847][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.848][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.849][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:03.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:03.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.852][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:03.853][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:03.854][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.854][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.855][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:03.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:03.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.858][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:03.859][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:03.860][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.861][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:03.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:03.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.865][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:03.866][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:03.866][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.867][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.868][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:03.869][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.869][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.870][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.871][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:03.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.875][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:03.875][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:03.876][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.877][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:03.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:03.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.881][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:03.882][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:03.883][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.883][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.885][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:03.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:03.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.894][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:03.895][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:03.896][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.897][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.898][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:03.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:03.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.901][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:03.902][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:03.902][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.903][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.904][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:03.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:03.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:03.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:03.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:03.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:03.938][self$createEntryFromContent] Accession numbers: 134117. biodb.TRACE[2024-06-29 16:02:03.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:03.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:03.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:03.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:03.947][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:03.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:03.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:03.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:03.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:03.955][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:03.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:03.956][private$loadEntries] Creating entries from ids [1]: "138307". biodb.DEBUG[2024-06-29 16:02:03.957][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:03.958][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307". biodb.TRACE[2024-06-29 16:02:03.959][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:03.960][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:03.961][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:03.962][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:03.963][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:03.964][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:03.966][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:03.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:03.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:03.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:03.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:03.972][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:03.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:03.974][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307". biodb.DEBUG[2024-06-29 16:02:03.976][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:03.977][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:03.978][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307". biodb.TRACE[2024-06-29 16:02:04.319][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307). biodb.DEBUG[2024-06-29 16:02:04.662][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:04.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content" biodb.TRACE[2024-06-29 16:02:04.667][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request" biodb.TRACE[2024-06-29 16:02:04.669][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml" biodb.DEBUG[2024-06-29 16:02:04.670][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:04.671][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:04.672][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:04.673][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:04.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:04.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:04.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:04.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:04.681][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:04.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:04.683][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:04.684][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:04.685][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.685][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:04.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:04.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.689][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:04.690][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:04.691][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.691][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.692][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:04.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:04.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.695][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:04.696][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:04.697][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.697][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.698][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:04.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:04.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.701][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:04.702][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:04.703][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.703][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:04.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:04.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.707][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:04.708][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:04.709][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.709][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:04.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:04.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.713][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:04.714][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:04.715][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.716][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.717][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:04.717][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:04.718][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.719][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.720][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:04.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:04.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.723][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:04.724][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:04.724][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.725][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:04.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:04.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.729][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:04.730][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:04.731][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.731][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:04.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:04.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.735][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:04.736][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:04.737][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.737][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.738][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:04.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:04.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.741][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:04.742][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:04.743][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.750][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.751][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:04.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:04.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:04.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:04.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:04.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:04.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:04.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:04.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:04.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:04.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:04.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:04.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:04.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:04.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:04.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:04.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:04.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:04.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:04.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:04.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:04.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:04.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:04.785][self$createEntryFromContent] Accession numbers: 138307. biodb.TRACE[2024-06-29 16:02:04.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:04.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:04.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:04.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:04.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:04.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:04.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:04.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:04.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:04.794][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:04.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:04.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:04.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:04.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:04.802][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:04.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:04.803][private$loadEntries] Creating entries from ids [1]: "176803". biodb.DEBUG[2024-06-29 16:02:04.804][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:04.805][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803". biodb.TRACE[2024-06-29 16:02:04.806][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:04.807][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:04.808][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:04.808][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:04.809][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:04.810][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:04.812][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:04.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:04.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:04.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:04.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:04.819][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:04.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:04.820][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803". biodb.DEBUG[2024-06-29 16:02:04.822][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:04.823][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:04.824][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803". biodb.TRACE[2024-06-29 16:02:05.163][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803). biodb.DEBUG[2024-06-29 16:02:05.495][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:05.496][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content" biodb.TRACE[2024-06-29 16:02:05.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request" biodb.TRACE[2024-06-29 16:02:05.501][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml" biodb.DEBUG[2024-06-29 16:02:05.506][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:05.510][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:05.511][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:05.512][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:05.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:05.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:05.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:05.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:05.519][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:05.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:05.522][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:05.523][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:05.523][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.524][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:05.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:05.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.528][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:05.529][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:05.530][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.531][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.531][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:05.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:05.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.534][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:05.535][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:05.536][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.536][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:05.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:05.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.541][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:05.541][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:05.542][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.543][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:05.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:05.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.547][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:05.548][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:05.549][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.549][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:05.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:05.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.553][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:05.554][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:05.555][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.555][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.556][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:05.557][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:05.558][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.558][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.559][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:05.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:05.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.562][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:05.563][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:05.564][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.565][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:05.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:05.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.569][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:05.570][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:05.571][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.571][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.572][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:05.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:05.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.575][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:05.576][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:05.577][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.577][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.578][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:05.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:05.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.582][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:05.582][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:05.583][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.584][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.585][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:05.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:05.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:05.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:05.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:05.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:05.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:05.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:05.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:05.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:05.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:05.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:05.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:05.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:05.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:05.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:05.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:05.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:05.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:05.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:05.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:05.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:05.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:05.622][self$createEntryFromContent] Accession numbers: 176803. biodb.TRACE[2024-06-29 16:02:05.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:05.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:05.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:05.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:05.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:05.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:05.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:05.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:05.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:05.632][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:05.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:05.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:05.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:05.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:05.639][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:05.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:05.641][private$loadEntries] Creating entries from ids [1]: "176962". biodb.DEBUG[2024-06-29 16:02:05.641][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:05.643][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962". biodb.TRACE[2024-06-29 16:02:05.643][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:05.644][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:05.645][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:05.646][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:05.647][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:05.647][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:05.649][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:05.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:05.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:05.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:05.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:05.657][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:05.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:05.658][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962". biodb.DEBUG[2024-06-29 16:02:05.660][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:05.661][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:05.662][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962". biodb.TRACE[2024-06-29 16:02:06.001][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962). biodb.DEBUG[2024-06-29 16:02:06.333][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:06.335][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content" biodb.TRACE[2024-06-29 16:02:06.338][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request" biodb.TRACE[2024-06-29 16:02:06.340][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml" biodb.DEBUG[2024-06-29 16:02:06.341][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:06.342][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:06.343][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:06.344][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:06.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:06.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:06.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:06.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:06.358][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:06.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:06.361][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:06.361][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:06.362][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.363][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:06.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:06.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.366][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:06.367][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:06.368][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.368][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.369][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:06.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:06.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.372][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:06.373][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:06.374][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.374][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.375][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:06.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:06.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.379][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:06.379][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:06.380][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.381][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:06.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:06.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.384][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:06.385][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:06.386][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.387][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.387][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:06.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:06.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.390][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:06.391][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:06.392][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.392][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.393][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:06.394][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:06.395][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.395][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.396][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:06.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:06.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.399][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:06.400][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:06.400][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.401][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:06.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:06.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.405][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:06.406][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:06.406][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.407][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:06.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:06.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.411][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:06.412][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:06.412][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.413][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.414][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:06.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:06.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.417][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:06.417][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:06.418][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.419][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.420][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:06.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:06.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:06.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:06.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:06.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:06.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:06.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:06.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:06.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:06.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:06.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:06.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:06.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:06.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:06.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:06.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:06.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:06.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:06.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:06.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:06.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:06.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:06.457][self$createEntryFromContent] Accession numbers: 176962. biodb.TRACE[2024-06-29 16:02:06.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:06.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:06.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:06.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:06.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:06.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:06.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:06.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:06.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:06.466][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:06.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:06.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:06.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:06.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:06.473][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:06.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:06.474][private$loadEntries] Creating entries from ids [1]: "198655". biodb.DEBUG[2024-06-29 16:02:06.475][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:06.476][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655". biodb.TRACE[2024-06-29 16:02:06.477][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:06.478][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:06.479][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:06.480][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:06.480][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:06.481][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:06.483][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:06.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:06.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:06.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:06.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:06.490][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:06.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:06.491][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655". biodb.DEBUG[2024-06-29 16:02:06.493][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:06.494][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:06.495][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655". biodb.TRACE[2024-06-29 16:02:06.907][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655). biodb.DEBUG[2024-06-29 16:02:07.256][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:07.257][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content" biodb.TRACE[2024-06-29 16:02:07.260][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request" biodb.TRACE[2024-06-29 16:02:07.262][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml" biodb.DEBUG[2024-06-29 16:02:07.264][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:07.265][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:07.266][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:07.267][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:07.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:07.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:07.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:07.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:07.274][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:07.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:07.276][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:07.277][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:07.278][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.278][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:07.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:07.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.290][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:07.291][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:07.291][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.292][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.293][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:07.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:07.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.296][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:07.297][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:07.298][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.299][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.300][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:07.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:07.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.303][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:07.304][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:07.304][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.305][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.306][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:07.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:07.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.309][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:07.310][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:07.311][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.311][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:07.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:07.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.316][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:07.316][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:07.317][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.318][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.319][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:07.320][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:07.320][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.321][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.322][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:07.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:07.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.325][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:07.326][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:07.327][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.328][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:07.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:07.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.331][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:07.332][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:07.333][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.334][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:07.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:07.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.337][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.338][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:07.338][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:07.339][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.340][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.341][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:07.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:07.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.344][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:07.345][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:07.345][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.346][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.347][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:07.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:07.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:07.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:07.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:07.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:07.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:07.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:07.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:07.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:07.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:07.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:07.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:07.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:07.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:07.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:07.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:07.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:07.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:07.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:07.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:07.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:07.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:07.385][self$createEntryFromContent] Accession numbers: 198655. biodb.TRACE[2024-06-29 16:02:07.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:07.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:07.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:07.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:07.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:07.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:07.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:07.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:07.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:07.394][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:07.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:07.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:07.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:07.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:07.402][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:07.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:07.403][private$loadEntries] Creating entries from ids [1]: "215045". biodb.DEBUG[2024-06-29 16:02:07.404][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:07.406][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045". biodb.TRACE[2024-06-29 16:02:07.407][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:07.408][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:07.408][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:07.409][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:07.410][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:07.411][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:07.413][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:07.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:07.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:07.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:07.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:07.420][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:07.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:07.422][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045". biodb.DEBUG[2024-06-29 16:02:07.424][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:07.424][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:07.425][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045". biodb.TRACE[2024-06-29 16:02:07.781][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045). biodb.DEBUG[2024-06-29 16:02:08.131][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:08.132][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content" biodb.TRACE[2024-06-29 16:02:08.135][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request" biodb.TRACE[2024-06-29 16:02:08.137][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml" biodb.DEBUG[2024-06-29 16:02:08.138][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:08.139][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:08.140][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:08.141][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.149][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.151][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:08.152][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:08.153][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.154][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:08.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:08.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.158][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:08.159][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:08.159][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.160][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.161][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:08.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:08.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.292][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:08.293][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:08.293][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.294][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:08.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:08.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.297][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.298][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:08.299][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:08.300][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.300][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:08.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:08.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.304][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:08.304][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:08.305][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.306][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:08.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:08.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.310][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:08.310][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:08.311][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.312][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.313][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:08.313][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.314][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.315][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.316][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:08.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.319][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.320][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.320][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.321][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.325][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:08.325][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:08.326][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.327][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:08.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:08.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.331][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:08.331][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:08.332][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.333][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.334][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:08.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:08.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.337][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:08.338][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:08.338][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.339][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.340][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:08.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:08.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:08.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:08.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:08.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:08.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:08.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:08.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:08.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:08.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:08.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:08.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:08.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:08.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:08.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:08.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:08.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:08.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:08.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:08.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:08.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:08.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.372][self$createEntryFromContent] Accession numbers: 215045. biodb.TRACE[2024-06-29 16:02:08.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.397][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:08.400][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:08.401][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-06-29 16:02:08.402][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:08.403][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-06-29 16:02:08.406][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.413][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.425][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.433][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.451][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.459][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.477][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.485][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.504][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.512][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.520][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.523][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.531][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.543][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.551][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.564][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.571][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.587][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.594][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.604][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.610][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.621][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.628][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.638][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.644][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.655][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.662][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.672][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.679][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.690][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.697][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.708][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.715][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.727][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.734][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.744][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.751][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.758][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.762][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.768][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.779][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:08.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:08.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:08.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:08.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:08.786][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:08.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:08.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:08.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:08.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:08.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:08.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:08.842][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:08.845][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:08.846][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:08.851][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:09.190][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:09.523][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:09.525][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content" biodb.TRACE[2024-06-29 16:02:09.528][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request" biodb.DEBUG[2024-06-29 16:02:09.531][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:09.533][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:09.534][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:09.535][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:09.898][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:10.231][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:10.233][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content" biodb.TRACE[2024-06-29 16:02:10.236][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request" biodb.DEBUG[2024-06-29 16:02:10.238][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:10.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:10.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:10.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:10.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:10.245][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:10.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:10.247][private$loadEntries] Creating entries from ids [1]: "4648". biodb.DEBUG[2024-06-29 16:02:10.247][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:10.249][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648". biodb.TRACE[2024-06-29 16:02:10.250][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:10.250][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:10.251][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:10.252][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:10.253][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:10.253][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:10.255][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:10.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:10.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:10.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:10.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:10.262][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:10.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:10.264][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648". biodb.DEBUG[2024-06-29 16:02:10.266][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:10.267][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:10.268][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648". biodb.TRACE[2024-06-29 16:02:10.614][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648). biodb.DEBUG[2024-06-29 16:02:10.951][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:10.953][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content" biodb.TRACE[2024-06-29 16:02:10.956][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request" biodb.TRACE[2024-06-29 16:02:10.958][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml" biodb.DEBUG[2024-06-29 16:02:10.959][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:10.960][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:10.960][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:10.961][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:10.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:10.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:10.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:10.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:10.968][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:10.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:10.970][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:10.971][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:10.972][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:10.972][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:10.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:10.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:10.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:10.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:10.976][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:10.977][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:10.978][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:10.978][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:10.979][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:10.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:10.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:10.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:10.982][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:10.983][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:10.983][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:10.984][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:10.985][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:10.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:10.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:10.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:10.988][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:10.989][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:10.989][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:10.990][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:10.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:10.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:10.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:10.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:10.994][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:10.995][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:10.995][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:10.996][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:10.997][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:10.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:10.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:10.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.000][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:11.000][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:11.001][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.002][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.003][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:11.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:11.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.005][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:11.006][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:11.007][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.008][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.008][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:11.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:11.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.011][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.012][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.013][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.013][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.017][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:11.018][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:11.019][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.019][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:11.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:11.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.023][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:11.024][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:11.025][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.025][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.026][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:11.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:11.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.029][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:11.030][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:11.031][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.032][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.033][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:11.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:11.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.065][self$createEntryFromContent] Accession numbers: 4648. biodb.TRACE[2024-06-29 16:02:11.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.075][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.082][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.093][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.100][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:11.101][private$loadEntries] Creating entries from ids [1]: "62447". biodb.DEBUG[2024-06-29 16:02:11.102][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:11.103][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447". biodb.TRACE[2024-06-29 16:02:11.104][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:11.106][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml". biodb.DEBUG[2024-06-29 16:02:11.107][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:11.108][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:11.109][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:11.110][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.117][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.119][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.120][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.120][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.121][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.125][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:11.126][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:11.127][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.127][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.128][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:11.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:11.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.131][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:11.132][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:11.133][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.133][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:11.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:11.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.137][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:11.138][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:11.138][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.139][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:11.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:11.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.143][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:11.143][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:11.144][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.145][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.146][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:11.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:11.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.149][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:11.149][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:11.150][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.151][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.152][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:11.153][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:11.153][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.154][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.155][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:11.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:11.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.168][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.169][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.170][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.170][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.174][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:11.175][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:11.175][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.176][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:11.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:11.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.180][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:11.180][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:11.181][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.182][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.183][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:11.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:11.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.186][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:11.186][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:11.187][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.188][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.189][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:11.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:11.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:11.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:11.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:11.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.221][self$createEntryFromContent] Accession numbers: 62447. biodb.TRACE[2024-06-29 16:02:11.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.246][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:11.249][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:11.250][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-06-29 16:02:11.251][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:11.252][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-06-29 16:02:11.254][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.261][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.271][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.278][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.293][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.300][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.316][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.323][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.339][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.346][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.357][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.364][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.374][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.381][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.392][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.399][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.409][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.416][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.426][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.437][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.448][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.455][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.465][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.472][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.483][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.490][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.500][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.506][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.517][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.524][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.535][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.542][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.552][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.559][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.570][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.576][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.586][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.593][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.604][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.611][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.637][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:11.640][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:11.641][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-06-29 16:02:11.642][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:11.643][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-06-29 16:02:11.645][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.652][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.663][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.670][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.688][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.695][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.716][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.716][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.722][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.739][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.746][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.757][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.764][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.775][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.782][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.793][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.801][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.813][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.822][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.834][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.842][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.854][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.861][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.871][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.878][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.888][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.895][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.905][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.912][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.922][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.929][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.939][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.945][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.956][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.963][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.973][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:11.979][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:11.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:11.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:11.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:11.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:11.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:11.989][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:11.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:11.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:11.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:11.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:12.000][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:12.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:12.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:12.010][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:12.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:12.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:12.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:12.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:12.016][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:12.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:12.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:12.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.040][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:02:12.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:02:12.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-29 16:02:12.049][biodb::testThat] biodb.INFO [2024-06-29 16:02:12.050][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. "). biodb.INFO [2024-06-29 16:02:12.051][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:02:12.051][biodb::testThat] biodb.TRACE[2024-06-29 16:02:12.053][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:12.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:12.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.056][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:12.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:12.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.059][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:12.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:12.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:12.098][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:12.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:12.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:12.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:12.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:12.105][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:12.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:12.108][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:12.110][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:12.111][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-06-29 16:02:12.112][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:12.113][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-06-29 16:02:12.115][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:12.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:12.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:12.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:12.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:12.121][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:12.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:12.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:12.132][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:12.134][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:12.135][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-06-29 16:02:12.136][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:12.137][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-06-29 16:02:12.139][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:12.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:12.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:12.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:12.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:12.146][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:12.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:12.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:12.156][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:12.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:12.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:12.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:12.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:12.163][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:12.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:12.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:12.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:12.173][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:12.174][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:12.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:12.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:12.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:12.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:12.181][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:12.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:12.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.188][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.189][private$selectFields] biodb.TRACE[2024-06-29 16:02:12.190][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:12.190][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:12.191][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.192][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.193][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.193][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.194][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.195][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.195][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.196][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.197][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.198][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.198][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.199][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.200][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.200][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.201][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.202][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:12.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.218][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2024-06-29 16:02:12.219][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:12.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:12.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:12.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:12.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:12.226][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:12.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:12.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.233][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.234][private$selectFields] biodb.TRACE[2024-06-29 16:02:12.234][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:12.235][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:12.236][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.236][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.237][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.238][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.239][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.239][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.240][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.241][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.241][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.242][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.243][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.244][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.244][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.245][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.246][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.246][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:12.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.261][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:02:12.261][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:12.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:12.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:12.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:12.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:12.268][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:12.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:12.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.275][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.276][private$selectFields] biodb.TRACE[2024-06-29 16:02:12.277][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:12.277][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:12.278][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.278][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.279][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.280][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.280][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.281][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.282][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.283][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.283][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.284][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.285][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:12.285][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.286][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.287][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.287][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.288][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:12.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:12.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:12.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:12.297][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2024-06-29 16:02:12.298][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:12.299][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:12.301][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:12.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:12.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:12.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:12.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:12.308][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:12.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:12.311][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:12.313][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:12.314][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:12.315][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:12.651][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:12.984][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:12.985][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content" biodb.TRACE[2024-06-29 16:02:12.988][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.request" biodb.DEBUG[2024-06-29 16:02:12.990][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:12.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:12.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:12.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:12.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:12.997][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:12.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:12.998][private$loadEntries] Creating entries from ids [1]: "113227". biodb.DEBUG[2024-06-29 16:02:12.999][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:13.000][cch$loadFileContent] Trying to load 1 files from cache: [1]: "113227". biodb.TRACE[2024-06-29 16:02:13.001][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:13.002][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:13.003][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:13.003][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:13.004][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:13.005][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:13.007][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:13.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:13.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:13.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:13.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:13.013][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:13.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:13.015][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=113227". biodb.DEBUG[2024-06-29 16:02:13.017][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:13.018][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:13.019][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=113227". biodb.TRACE[2024-06-29 16:02:13.360][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=113227). biodb.DEBUG[2024-06-29 16:02:13.694][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:13.696][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ed496dac459a2ba62e671edbcae22326.content" biodb.TRACE[2024-06-29 16:02:13.699][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ed496dac459a2ba62e671edbcae22326.request" biodb.TRACE[2024-06-29 16:02:13.701][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/113227.xml" biodb.DEBUG[2024-06-29 16:02:13.702][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:13.703][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:13.704][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:13.705][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:13.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:13.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:13.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:13.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:13.713][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:13.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:13.715][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:13.716][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:13.717][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.717][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:13.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:13.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.721][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:13.722][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:13.723][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.723][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.724][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:13.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:13.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.727][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:13.728][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:13.729][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.729][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.730][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:13.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:13.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.734][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:13.734][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:13.735][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.736][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:13.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:13.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.740][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:13.741][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:13.742][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.742][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:13.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:13.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.746][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:13.747][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:13.748][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.748][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.749][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:13.750][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:13.751][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.751][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.752][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:13.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:13.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.755][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:13.756][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:13.757][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.758][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:13.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:13.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.761][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:13.762][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:13.763][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.764][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:13.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:13.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.768][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:13.768][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:13.769][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.770][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.771][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:13.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:13.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.774][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:13.774][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:13.775][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.776][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.777][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:13.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:13.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:13.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:13.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:13.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:13.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:13.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:13.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:13.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:13.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:13.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:13.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:13.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:13.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:13.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:13.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:13.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:13.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:13.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:13.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:13.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:13.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:13.809][self$createEntryFromContent] Accession numbers: 113227. biodb.TRACE[2024-06-29 16:02:13.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:13.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:13.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:13.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:13.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:13.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:13.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:13.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:13.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:13.818][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:13.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:13.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:13.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:13.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:13.825][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:13.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:13.827][private$loadEntries] Creating entries from ids [1]: "169712". biodb.DEBUG[2024-06-29 16:02:13.827][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:13.829][cch$loadFileContent] Trying to load 1 files from cache: [1]: "169712". biodb.TRACE[2024-06-29 16:02:13.830][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:13.831][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:13.831][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:13.832][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:13.833][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:13.834][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:13.836][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:13.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:13.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:13.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:13.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:13.842][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:13.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:13.844][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169712". biodb.DEBUG[2024-06-29 16:02:13.846][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:13.846][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:13.847][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169712". biodb.TRACE[2024-06-29 16:02:14.188][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169712). biodb.DEBUG[2024-06-29 16:02:14.523][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:14.525][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6e52d7b9d801aec68d97cc03bd4acc90.content" biodb.TRACE[2024-06-29 16:02:14.527][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6e52d7b9d801aec68d97cc03bd4acc90.request" biodb.TRACE[2024-06-29 16:02:14.529][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/169712.xml" biodb.DEBUG[2024-06-29 16:02:14.530][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:14.542][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:14.543][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:14.544][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:14.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:14.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:14.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:14.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:14.550][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:14.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:14.553][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:14.554][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:14.554][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.555][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:14.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:14.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.559][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:14.559][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:14.560][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.561][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.562][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:14.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:14.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.565][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:14.565][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:14.566][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.567][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:14.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:14.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.571][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:14.571][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:14.572][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.573][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:14.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:14.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.577][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:14.577][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:14.578][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.579][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:14.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:14.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.583][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:14.583][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:14.584][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.585][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.586][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:14.586][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:14.587][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.588][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.589][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:14.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:14.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.592][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:14.593][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:14.593][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.594][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:14.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:14.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.598][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:14.598][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:14.599][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.600][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.601][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:14.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:14.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.604][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:14.604][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:14.605][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.606][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.606][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:14.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:14.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.609][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:14.610][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:14.611][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.611][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.612][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:14.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:14.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:14.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:14.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:14.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:14.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:14.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:14.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:14.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:14.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:14.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:14.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:14.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:14.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:14.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:14.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:14.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:14.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:14.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:14.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:14.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:14.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:14.644][self$createEntryFromContent] Accession numbers: 169712. biodb.TRACE[2024-06-29 16:02:14.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:14.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:14.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:14.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:14.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.650][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:14.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:14.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:14.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:14.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:14.654][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:14.656][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:14.657][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:14.658][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:14.993][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:15.328][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:15.330][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content" biodb.TRACE[2024-06-29 16:02:15.333][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.request" biodb.DEBUG[2024-06-29 16:02:15.335][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:15.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:15.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:15.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:15.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:15.342][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:15.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:15.344][private$loadEntries] Creating entries from ids [1]: "4781". biodb.DEBUG[2024-06-29 16:02:15.345][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:15.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4781". biodb.TRACE[2024-06-29 16:02:15.347][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:15.348][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:15.348][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:15.349][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:15.350][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:15.351][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:15.353][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:15.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:15.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:15.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:15.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:15.359][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:15.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:15.361][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4781". biodb.DEBUG[2024-06-29 16:02:15.363][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:15.364][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:15.365][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4781". biodb.TRACE[2024-06-29 16:02:15.718][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4781). biodb.DEBUG[2024-06-29 16:02:16.137][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:16.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e4869054c906476bc1e4ece10c7e53cc.content" biodb.TRACE[2024-06-29 16:02:16.141][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e4869054c906476bc1e4ece10c7e53cc.request" biodb.TRACE[2024-06-29 16:02:16.143][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4781.xml" biodb.DEBUG[2024-06-29 16:02:16.145][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:16.145][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:16.146][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:16.148][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:16.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:16.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:16.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:16.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:16.155][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:16.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:16.157][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:16.158][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:16.158][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.159][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:16.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:16.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.163][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:16.164][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:16.164][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.165][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.166][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:16.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:16.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.169][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:16.170][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:16.170][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.171][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.172][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:16.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:16.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.175][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:16.176][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:16.176][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.177][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:16.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:16.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.181][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:16.182][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:16.182][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.183][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:16.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:16.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.187][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:16.188][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:16.189][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.189][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.190][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:16.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:16.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.193][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:16.194][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:16.195][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.195][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.196][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:16.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:16.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.199][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:16.200][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:16.201][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.201][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:16.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:16.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.205][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:16.206][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:16.207][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.207][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.208][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:16.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:16.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.211][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:16.212][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:16.213][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.213][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.214][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:16.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:16.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.218][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:16.218][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:16.219][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.220][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.221][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:16.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:16.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:16.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:16.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:16.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:16.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:16.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:16.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:16.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:16.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:16.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:16.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:16.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:16.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:16.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:16.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:16.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:16.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:16.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:16.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:16.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:16.260][self$createEntryFromContent] Accession numbers: 4781. biodb.TRACE[2024-06-29 16:02:16.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:16.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:16.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:16.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:16.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:16.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:16.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:16.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:16.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:16.270][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:16.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:16.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:16.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:16.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:16.276][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:16.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:16.278][private$loadEntries] Creating entries from ids [1]: "16587". biodb.DEBUG[2024-06-29 16:02:16.278][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:16.279][cch$loadFileContent] Trying to load 1 files from cache: [1]: "16587". biodb.TRACE[2024-06-29 16:02:16.280][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:16.281][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:16.282][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:16.283][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:16.283][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:16.284][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:16.286][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:16.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:16.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:16.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:16.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:16.293][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:16.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:16.294][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=16587". biodb.DEBUG[2024-06-29 16:02:16.296][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:16.297][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:16.298][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=16587". biodb.TRACE[2024-06-29 16:02:16.663][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=16587). biodb.DEBUG[2024-06-29 16:02:17.015][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:17.016][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6012905c0932919c069ecb5afc0b487b.content" biodb.TRACE[2024-06-29 16:02:17.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6012905c0932919c069ecb5afc0b487b.request" biodb.TRACE[2024-06-29 16:02:17.021][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/16587.xml" biodb.DEBUG[2024-06-29 16:02:17.022][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:17.023][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:17.024][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:17.025][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:17.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:17.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:17.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:17.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:17.032][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:17.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:17.034][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.035][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.035][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.036][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.040][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:17.041][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:17.041][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.042][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.043][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:17.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:17.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.046][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:17.047][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:17.047][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.048][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.049][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:17.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:17.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.052][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:17.053][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:17.054][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.054][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:17.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:17.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.058][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:17.059][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:17.060][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.061][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:17.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:17.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.065][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:17.065][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:17.066][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.067][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.068][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:17.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:17.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.071][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:17.071][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.072][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.073][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.074][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:17.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.077][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:17.077][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:17.078][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.079][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:17.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:17.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.083][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:17.084][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:17.084][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.085][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:17.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:17.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.089][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:17.090][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:17.091][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.092][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.093][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:17.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:17.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.096][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:17.096][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:17.097][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.098][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.099][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:17.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:17.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:17.131][self$createEntryFromContent] Accession numbers: 16587. biodb.TRACE[2024-06-29 16:02:17.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:17.141][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:17.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:17.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:17.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:17.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:17.148][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:17.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:17.150][private$loadEntries] Creating entries from ids [1]: "19804". biodb.DEBUG[2024-06-29 16:02:17.150][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:17.151][cch$loadFileContent] Trying to load 1 files from cache: [1]: "19804". biodb.TRACE[2024-06-29 16:02:17.152][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:17.153][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:17.154][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:17.155][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:17.155][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:17.156][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:17.158][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:17.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:17.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:17.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:17.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:17.165][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:17.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:17.167][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=19804". biodb.DEBUG[2024-06-29 16:02:17.169][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:17.169][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:17.170][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=19804". biodb.TRACE[2024-06-29 16:02:17.514][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=19804). biodb.DEBUG[2024-06-29 16:02:17.851][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:17.852][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ef7e014212775cbaa9299e60f32b2bcd.content" biodb.TRACE[2024-06-29 16:02:17.855][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ef7e014212775cbaa9299e60f32b2bcd.request" biodb.TRACE[2024-06-29 16:02:17.857][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/19804.xml" biodb.DEBUG[2024-06-29 16:02:17.859][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:17.860][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:17.860][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:17.862][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:17.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:17.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:17.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:17.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:17.869][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:17.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:17.871][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.872][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.873][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.874][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.877][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:17.878][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:17.879][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.880][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.880][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:17.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:17.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.883][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:17.884][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:17.885][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.885][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.886][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:17.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:17.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.889][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:17.890][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:17.891][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.891][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:17.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:17.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.904][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:17.904][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:17.905][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.906][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.906][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:17.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:17.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.909][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:17.910][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:17.911][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.911][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.912][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:17.913][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.914][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.914][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.915][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:17.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.918][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:17.919][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:17.919][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.920][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:17.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:17.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.924][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:17.924][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:17.925][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.926][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:17.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:17.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.930][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:17.931][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:17.931][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.932][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.933][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:17.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:17.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.936][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:17.937][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:17.937][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.938][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.939][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:17.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:17.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:17.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:17.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:17.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:17.970][self$createEntryFromContent] Accession numbers: 19804. biodb.TRACE[2024-06-29 16:02:17.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:17.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:17.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:17.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:17.996][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:18.013][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:18.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:18.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:18.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:18.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:18.020][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:18.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:18.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.028][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.028][private$selectFields] biodb.TRACE[2024-06-29 16:02:18.029][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:18.030][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:18.030][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.031][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.032][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.033][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.033][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.034][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.035][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.035][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.036][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.037][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.038][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.038][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.039][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.040][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.041][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.041][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:18.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.051][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:02:18.052][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:18.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:18.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:18.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:18.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:18.059][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:18.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:18.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.067][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.068][private$selectFields] biodb.TRACE[2024-06-29 16:02:18.068][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:18.069][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:18.070][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.070][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.071][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.072][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.073][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.073][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.074][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.075][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.075][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.076][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.077][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.077][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.078][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.079][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.080][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.080][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:18.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.090][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-06-29 16:02:18.091][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:18.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:18.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:18.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:18.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:18.098][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:18.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:18.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.105][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.106][private$selectFields] biodb.TRACE[2024-06-29 16:02:18.107][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:18.107][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:18.108][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.109][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.110][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.110][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.111][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.112][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.113][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.113][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.114][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.115][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.116][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:18.116][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.117][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.118][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.119][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.120][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:18.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:18.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:18.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:18.129][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-06-29 16:02:18.130][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:18.131][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:18.132][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:18.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:18.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:18.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:18.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:18.143][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:18.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:18.146][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:18.148][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:18.148][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:18.150][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:18.486][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:18.823][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:18.825][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content" biodb.TRACE[2024-06-29 16:02:18.828][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.request" biodb.DEBUG[2024-06-29 16:02:18.830][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:18.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:18.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:18.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:18.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:18.837][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:18.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:18.839][private$loadEntries] Creating entries from ids [1]: "159630". biodb.DEBUG[2024-06-29 16:02:18.840][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:18.841][cch$loadFileContent] Trying to load 1 files from cache: [1]: "159630". biodb.TRACE[2024-06-29 16:02:18.842][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:18.842][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:18.843][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:18.844][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:18.845][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:18.845][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:18.847][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:18.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:18.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:18.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:18.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:18.855][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:18.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:18.856][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=159630". biodb.DEBUG[2024-06-29 16:02:18.858][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:18.859][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:18.860][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=159630". biodb.TRACE[2024-06-29 16:02:19.244][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=159630). biodb.DEBUG[2024-06-29 16:02:19.585][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:19.587][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f9497c6792bdb2528746e6a81b02589e.content" biodb.TRACE[2024-06-29 16:02:19.590][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f9497c6792bdb2528746e6a81b02589e.request" biodb.TRACE[2024-06-29 16:02:19.592][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/159630.xml" biodb.DEBUG[2024-06-29 16:02:19.593][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:19.594][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:19.595][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:19.596][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:19.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:19.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:19.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:19.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:19.603][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:19.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:19.606][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:19.606][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:19.607][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.608][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:19.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:19.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.612][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:19.612][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:19.613][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.614][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.615][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:19.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:19.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.618][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:19.618][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:19.619][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.620][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.621][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:19.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:19.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.624][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:19.625][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:19.625][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.626][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:19.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:19.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.630][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:19.631][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:19.631][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.632][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:19.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:19.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.636][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:19.637][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:19.638][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.638][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.639][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:19.640][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:19.641][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.641][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.642][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:19.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:19.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.646][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:19.646][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:19.647][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.648][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:19.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:19.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.652][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:19.652][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:19.653][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.654][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:19.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:19.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.658][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:19.658][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:19.659][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.660][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.661][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:19.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:19.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.663][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:19.664][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:19.665][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.666][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.666][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:19.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:19.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:19.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:19.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:19.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:19.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:19.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:19.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:19.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:19.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:19.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:19.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:19.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:19.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:19.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:19.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:19.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:19.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:19.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:19.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:19.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:19.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:19.699][self$createEntryFromContent] Accession numbers: 159630. biodb.TRACE[2024-06-29 16:02:19.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:19.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:19.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:19.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:19.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:19.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:19.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:19.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:19.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:19.708][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:19.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:19.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:19.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:19.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:19.715][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:19.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:19.716][private$loadEntries] Creating entries from ids [1]: "160202". biodb.DEBUG[2024-06-29 16:02:19.717][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:19.718][cch$loadFileContent] Trying to load 1 files from cache: [1]: "160202". biodb.TRACE[2024-06-29 16:02:19.719][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:19.720][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:19.721][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:19.721][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:19.722][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:19.723][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:19.725][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:19.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:19.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:19.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:19.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:19.732][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:19.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:19.733][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160202". biodb.DEBUG[2024-06-29 16:02:19.735][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:19.736][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:19.737][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160202". biodb.TRACE[2024-06-29 16:02:20.079][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160202). biodb.DEBUG[2024-06-29 16:02:20.414][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:20.416][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1de9586ccaafdf8e637928dc3e313d63.content" biodb.TRACE[2024-06-29 16:02:20.418][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1de9586ccaafdf8e637928dc3e313d63.request" biodb.TRACE[2024-06-29 16:02:20.420][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/160202.xml" biodb.DEBUG[2024-06-29 16:02:20.421][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:20.422][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:20.423][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:20.424][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:20.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:20.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:20.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:20.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:20.431][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:20.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:20.433][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:20.433][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:20.434][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.435][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:20.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:20.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.439][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:20.440][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:20.441][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.441][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.442][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:20.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:20.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.445][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:20.446][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:20.447][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.447][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.448][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:20.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:20.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.451][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:20.452][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:20.453][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.454][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.455][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:20.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:20.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.458][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:20.458][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:20.459][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.460][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.460][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:20.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:20.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.463][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:20.464][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:20.465][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.465][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.466][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:20.467][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:20.468][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.468][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.469][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:20.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:20.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.483][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:20.484][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:20.484][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.485][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:20.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:20.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.488][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:20.489][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:20.490][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.490][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:20.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:20.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.494][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:20.495][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:20.496][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.496][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.497][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:20.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:20.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.500][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:20.501][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:20.501][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.502][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.503][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:20.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:20.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:20.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:20.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:20.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:20.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:20.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:20.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:20.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:20.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:20.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:20.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:20.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:20.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:20.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:20.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:20.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:20.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:20.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:20.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:20.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:20.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:20.533][self$createEntryFromContent] Accession numbers: 160202. biodb.TRACE[2024-06-29 16:02:20.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:20.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:20.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:20.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:20.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:20.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:20.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:20.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:20.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:20.542][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:20.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:20.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:20.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:20.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:20.549][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:20.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:20.550][private$loadEntries] Creating entries from ids [1]: "160393". biodb.DEBUG[2024-06-29 16:02:20.551][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:20.552][cch$loadFileContent] Trying to load 1 files from cache: [1]: "160393". biodb.TRACE[2024-06-29 16:02:20.553][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:20.554][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:20.555][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:20.556][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:20.556][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:20.557][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:20.559][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:20.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:20.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:20.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:20.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:20.566][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:20.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:20.568][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160393". biodb.DEBUG[2024-06-29 16:02:20.570][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:20.571][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:20.572][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160393". biodb.TRACE[2024-06-29 16:02:20.914][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160393). biodb.DEBUG[2024-06-29 16:02:21.271][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:21.273][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e0266c32050b31cda3d5e01c2d907fcd.content" biodb.TRACE[2024-06-29 16:02:21.276][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e0266c32050b31cda3d5e01c2d907fcd.request" biodb.TRACE[2024-06-29 16:02:21.278][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/160393.xml" biodb.DEBUG[2024-06-29 16:02:21.279][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:21.280][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:21.280][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:21.282][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:21.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:21.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:21.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:21.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:21.289][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:21.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:21.291][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:21.292][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:21.292][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.293][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:21.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:21.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.297][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:21.298][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:21.298][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.299][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.300][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:21.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:21.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.303][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:21.304][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:21.304][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.305][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.306][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:21.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:21.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.309][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:21.310][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:21.310][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.311][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:21.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:21.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.315][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:21.316][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:21.317][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.317][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.318][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:21.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:21.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.321][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:21.322][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:21.323][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.323][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.324][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:21.325][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:21.326][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.327][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.328][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:21.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:21.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.331][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:21.332][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:21.332][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.333][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:21.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:21.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.337][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:21.337][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:21.338][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.339][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:21.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:21.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.343][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:21.344][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:21.345][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.346][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.347][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:21.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:21.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.350][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:21.351][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:21.351][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.352][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.353][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:21.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:21.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:21.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:21.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:21.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:21.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:21.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:21.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:21.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:21.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:21.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:21.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:21.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:21.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:21.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:21.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:21.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:21.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:21.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:21.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:21.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:21.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:21.385][self$createEntryFromContent] Accession numbers: 160393. biodb.TRACE[2024-06-29 16:02:21.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:21.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:21.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:21.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:21.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:21.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:21.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:21.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:21.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:21.394][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:21.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:21.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:21.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:21.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:21.401][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:21.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:21.402][private$loadEntries] Creating entries from ids [1]: "160991". biodb.DEBUG[2024-06-29 16:02:21.403][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:21.404][cch$loadFileContent] Trying to load 1 files from cache: [1]: "160991". biodb.TRACE[2024-06-29 16:02:21.405][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:21.406][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:21.406][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:21.407][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:21.408][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:21.409][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:21.411][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:21.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:21.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:21.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:21.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:21.417][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:21.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:21.419][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160991". biodb.DEBUG[2024-06-29 16:02:21.421][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:21.422][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:21.423][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160991". biodb.TRACE[2024-06-29 16:02:21.761][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160991). biodb.DEBUG[2024-06-29 16:02:22.095][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:22.097][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6bad8d3e957240d90a71edc1329f8f37.content" biodb.TRACE[2024-06-29 16:02:22.100][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6bad8d3e957240d90a71edc1329f8f37.request" biodb.TRACE[2024-06-29 16:02:22.111][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/160991.xml" biodb.DEBUG[2024-06-29 16:02:22.113][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:22.114][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:22.115][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:22.116][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:22.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:22.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:22.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:22.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:22.123][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:22.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:22.125][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:22.126][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:22.127][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.127][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:22.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:22.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.131][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:22.132][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:22.132][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.133][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.134][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:22.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:22.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.137][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:22.138][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:22.139][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.139][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.140][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:22.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:22.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.143][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:22.144][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:22.145][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.145][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.146][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:22.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:22.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.150][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:22.150][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:22.151][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.152][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.153][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:22.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:22.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.156][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:22.156][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:22.157][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.158][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.159][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:22.159][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:22.160][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.161][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.162][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:22.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:22.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.165][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:22.165][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:22.166][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.167][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:22.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:22.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.170][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:22.171][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:22.172][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.172][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:22.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:22.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.177][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:22.177][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:22.178][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.179][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.179][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:22.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:22.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.182][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:22.183][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:22.184][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.184][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.185][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:22.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:22.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:22.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:22.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:22.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:22.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:22.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:22.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:22.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:22.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:22.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:22.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:22.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:22.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:22.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:22.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:22.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:22.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:22.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:22.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:22.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:22.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:22.218][self$createEntryFromContent] Accession numbers: 160991. biodb.TRACE[2024-06-29 16:02:22.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:22.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:22.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:22.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:22.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:22.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:22.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:22.227][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:22.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:22.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:22.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:22.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:22.234][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:22.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:22.235][private$loadEntries] Creating entries from ids [1]: "164975". biodb.DEBUG[2024-06-29 16:02:22.236][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:22.237][cch$loadFileContent] Trying to load 1 files from cache: [1]: "164975". biodb.TRACE[2024-06-29 16:02:22.238][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:22.239][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:22.240][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:22.241][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:22.242][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:22.243][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:22.245][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:22.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:22.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:22.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:22.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:22.252][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:22.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:22.253][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164975". biodb.DEBUG[2024-06-29 16:02:22.255][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:22.256][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:22.257][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164975". biodb.TRACE[2024-06-29 16:02:22.599][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164975). biodb.DEBUG[2024-06-29 16:02:22.935][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:22.937][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b1cbfaf7aef2d62dc8db3306c1521943.content" biodb.TRACE[2024-06-29 16:02:22.940][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b1cbfaf7aef2d62dc8db3306c1521943.request" biodb.TRACE[2024-06-29 16:02:22.942][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/164975.xml" biodb.DEBUG[2024-06-29 16:02:22.943][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:22.944][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:22.945][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:22.947][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:22.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:22.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:22.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:22.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:22.954][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:22.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:22.957][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:22.958][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:22.958][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.959][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:22.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:22.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.963][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:22.964][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:22.965][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.966][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.967][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:22.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:22.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.970][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:22.971][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:22.971][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.972][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.973][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:22.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:22.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.976][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:22.977][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:22.978][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.978][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.979][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:22.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:22.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.982][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:22.983][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:22.984][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.984][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.985][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:22.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:22.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.988][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:22.989][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:22.990][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.991][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.992][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:22.992][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:22.993][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.994][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.995][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:22.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:22.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:22.997][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:22.998][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:22.999][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:22.999][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:23.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:23.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.003][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:23.004][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:23.004][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.005][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.006][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:23.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:23.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.009][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:23.010][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:23.010][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.011][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.012][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:23.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:23.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.015][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:23.015][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:23.016][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.017][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.018][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:23.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:23.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:23.057][self$createEntryFromContent] Accession numbers: 164975. biodb.TRACE[2024-06-29 16:02:23.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:23.066][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:23.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:23.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:23.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:23.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:23.072][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:23.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:23.074][private$loadEntries] Creating entries from ids [1]: "164994". biodb.DEBUG[2024-06-29 16:02:23.075][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:23.076][cch$loadFileContent] Trying to load 1 files from cache: [1]: "164994". biodb.TRACE[2024-06-29 16:02:23.077][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:23.077][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:23.078][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:23.079][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:23.079][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:23.080][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:23.082][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:23.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:23.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:23.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:23.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:23.089][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:23.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:23.090][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164994". biodb.DEBUG[2024-06-29 16:02:23.092][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:23.093][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:23.094][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164994". biodb.TRACE[2024-06-29 16:02:23.437][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164994). biodb.DEBUG[2024-06-29 16:02:23.771][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:23.773][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c2789f33696a1a62a1d6cd81e3041cd1.content" biodb.TRACE[2024-06-29 16:02:23.775][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c2789f33696a1a62a1d6cd81e3041cd1.request" biodb.TRACE[2024-06-29 16:02:23.777][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/164994.xml" biodb.DEBUG[2024-06-29 16:02:23.779][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:23.779][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:23.780][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:23.781][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:23.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:23.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:23.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:23.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:23.788][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:23.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:23.791][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.791][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.792][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.793][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.796][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:23.797][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:23.798][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.799][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.800][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:23.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:23.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.802][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:23.803][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:23.804][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.805][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.806][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:23.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:23.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.809][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:23.810][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:23.810][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.811][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:23.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:23.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.815][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:23.816][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:23.817][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.817][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:23.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:23.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.821][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:23.822][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:23.823][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.824][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.825][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:23.825][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.826][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.827][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.828][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:23.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.831][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:23.831][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:23.832][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.833][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:23.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:23.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.837][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:23.838][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:23.838][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.839][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:23.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:23.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.843][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:23.844][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:23.844][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.845][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.846][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:23.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:23.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.849][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:23.850][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:23.850][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.851][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.852][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:23.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:23.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:23.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:23.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:23.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:23.885][self$createEntryFromContent] Accession numbers: 164994. biodb.TRACE[2024-06-29 16:02:23.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:23.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:23.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:23.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:23.895][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:23.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:23.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:23.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:23.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:23.902][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:23.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:23.903][private$loadEntries] Creating entries from ids [1]: "169251". biodb.DEBUG[2024-06-29 16:02:23.904][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:23.905][cch$loadFileContent] Trying to load 1 files from cache: [1]: "169251". biodb.TRACE[2024-06-29 16:02:23.906][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:23.907][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:23.908][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:23.909][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:23.910][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:23.910][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:23.912][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:23.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:23.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:23.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:23.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:23.919][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:23.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:23.921][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169251". biodb.DEBUG[2024-06-29 16:02:23.923][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:23.924][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:23.925][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169251". biodb.TRACE[2024-06-29 16:02:24.264][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169251). biodb.DEBUG[2024-06-29 16:02:24.600][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:24.602][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/06c85ce8d5c9a410c27ad425a575abe7.content" biodb.TRACE[2024-06-29 16:02:24.605][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/06c85ce8d5c9a410c27ad425a575abe7.request" biodb.TRACE[2024-06-29 16:02:24.607][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/169251.xml" biodb.DEBUG[2024-06-29 16:02:24.608][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:24.609][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:24.609][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:24.611][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:24.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:24.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:24.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:24.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:24.617][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:24.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:24.619][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:24.620][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:24.621][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.621][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:24.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:24.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.626][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:24.626][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:24.627][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.628][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.629][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:24.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:24.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.631][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:24.632][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:24.633][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.634][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.635][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:24.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:24.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.637][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:24.638][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:24.639][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.639][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.640][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:24.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:24.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.643][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:24.644][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:24.645][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.645][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:24.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:24.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.649][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:24.650][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:24.650][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.651][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.652][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:24.653][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:24.657][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.663][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.663][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:24.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:24.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.666][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:24.667][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:24.668][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.668][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:24.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:24.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.672][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:24.673][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:24.673][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.674][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.675][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:24.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:24.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.678][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:24.679][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:24.680][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.680][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.681][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:24.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:24.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.684][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:24.685][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:24.685][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.686][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.687][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:24.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:24.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:24.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:24.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:24.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:24.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:24.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:24.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:24.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:24.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:24.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:24.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:24.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:24.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:24.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:24.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:24.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:24.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:24.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:24.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:24.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:24.717][self$createEntryFromContent] Accession numbers: 169251. biodb.TRACE[2024-06-29 16:02:24.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:24.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:24.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:24.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:24.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:24.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:24.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:24.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:24.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:24.726][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:24.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:24.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:24.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:24.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:24.733][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:24.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:24.734][private$loadEntries] Creating entries from ids [1]: "224261". biodb.DEBUG[2024-06-29 16:02:24.735][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:24.736][cch$loadFileContent] Trying to load 1 files from cache: [1]: "224261". biodb.TRACE[2024-06-29 16:02:24.737][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:24.738][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:24.739][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:24.739][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:24.740][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:24.741][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:24.743][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:24.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:24.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:24.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:24.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:24.750][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:24.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:24.751][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=224261". biodb.DEBUG[2024-06-29 16:02:24.753][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:24.754][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:24.755][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=224261". biodb.TRACE[2024-06-29 16:02:25.094][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=224261). biodb.DEBUG[2024-06-29 16:02:25.437][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:25.439][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7ba99c29fa5d3888a543698650c3997e.content" biodb.TRACE[2024-06-29 16:02:25.442][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7ba99c29fa5d3888a543698650c3997e.request" biodb.TRACE[2024-06-29 16:02:25.443][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/224261.xml" biodb.DEBUG[2024-06-29 16:02:25.445][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:25.445][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:25.446][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:25.447][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:25.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:25.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:25.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:25.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:25.454][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:25.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:25.456][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:25.457][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:25.458][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.458][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:25.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:25.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.462][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:25.463][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:25.463][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.464][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.465][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:25.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:25.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.468][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:25.468][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:25.469][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.470][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:25.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:25.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.474][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:25.474][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:25.475][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.476][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:25.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:25.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.479][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:25.480][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:25.481][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.481][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:25.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:25.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.485][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:25.486][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:25.486][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.487][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.488][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:25.489][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:25.489][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.490][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.491][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:25.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:25.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.494][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:25.494][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:25.495][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.496][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:25.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:25.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.499][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:25.500][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:25.501][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.501][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:25.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:25.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.505][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:25.506][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:25.507][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.507][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.508][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:25.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:25.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.511][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:25.512][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:25.512][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.513][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.514][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:25.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:25.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:25.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:25.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:25.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:25.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:25.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:25.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:25.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:25.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:25.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:25.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:25.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:25.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:25.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:25.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:25.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:25.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:25.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:25.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:25.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:25.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:25.545][self$createEntryFromContent] Accession numbers: 224261. biodb.TRACE[2024-06-29 16:02:25.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:25.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:25.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:25.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:25.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:25.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:25.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:25.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:25.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:25.555][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:25.557][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:25.558][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:25.559][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:25.897][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:26.235][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:26.237][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content" biodb.TRACE[2024-06-29 16:02:26.240][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.request" biodb.DEBUG[2024-06-29 16:02:26.243][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:26.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:26.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:26.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:26.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:26.250][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:26.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:26.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:26.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:26.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:26.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:26.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:26.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:26.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:26.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:26.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:26.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:26.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:26.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:26.261][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:26.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:26.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:26.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:26.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:26.278][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:26.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:26.279][private$loadEntries] Creating entries from ids [1]: "71954". biodb.DEBUG[2024-06-29 16:02:26.280][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:26.281][cch$loadFileContent] Trying to load 1 files from cache: [1]: "71954". biodb.TRACE[2024-06-29 16:02:26.282][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:26.283][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:26.284][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:26.284][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:26.285][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:26.286][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:26.288][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:26.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:26.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:26.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:26.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:26.294][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:26.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:26.296][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71954". biodb.DEBUG[2024-06-29 16:02:26.298][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:26.299][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:26.299][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71954". biodb.TRACE[2024-06-29 16:02:26.642][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71954). biodb.DEBUG[2024-06-29 16:02:26.979][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:26.981][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/58f24f0de3d9b6c69a2b349522c5c9b3.content" biodb.TRACE[2024-06-29 16:02:26.983][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/58f24f0de3d9b6c69a2b349522c5c9b3.request" biodb.TRACE[2024-06-29 16:02:26.985][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/71954.xml" biodb.DEBUG[2024-06-29 16:02:26.986][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:26.987][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:26.988][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:26.989][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:26.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:26.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:26.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:26.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:26.996][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:26.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:26.998][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:26.999][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.000][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.001][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.004][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:27.005][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:27.006][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.006][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.007][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:27.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:27.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.010][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:27.011][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:27.011][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.012][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.013][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:27.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:27.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.016][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:27.016][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:27.017][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.018][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:27.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:27.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.021][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:27.022][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:27.023][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.024][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:27.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:27.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.027][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:27.028][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:27.029][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.029][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.030][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:27.031][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.032][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.032][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.033][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:27.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.036][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:27.037][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:27.038][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.038][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:27.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:27.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.042][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:27.043][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:27.044][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.044][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:27.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:27.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.048][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:27.049][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:27.050][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.050][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.051][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:27.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:27.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.054][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:27.055][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:27.056][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.056][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.057][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:27.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:27.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:27.089][self$createEntryFromContent] Accession numbers: 71954. biodb.TRACE[2024-06-29 16:02:27.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:27.099][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:27.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:27.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:27.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:27.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:27.106][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:27.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:27.108][private$loadEntries] Creating entries from ids [1]: "197612". biodb.DEBUG[2024-06-29 16:02:27.109][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:27.110][cch$loadFileContent] Trying to load 1 files from cache: [1]: "197612". biodb.TRACE[2024-06-29 16:02:27.111][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:27.112][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:27.113][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:27.113][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:27.114][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:27.115][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:27.117][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:27.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:27.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:27.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:27.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:27.124][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:27.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:27.125][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=197612". biodb.DEBUG[2024-06-29 16:02:27.127][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:27.128][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:27.129][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=197612". biodb.TRACE[2024-06-29 16:02:27.468][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=197612). biodb.DEBUG[2024-06-29 16:02:27.802][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:27.804][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d602b140c80212c04a1a2ba98ef7dc4f.content" biodb.TRACE[2024-06-29 16:02:27.807][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d602b140c80212c04a1a2ba98ef7dc4f.request" biodb.TRACE[2024-06-29 16:02:27.809][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/197612.xml" biodb.DEBUG[2024-06-29 16:02:27.811][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:27.812][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:27.812][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:27.814][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:27.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:27.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:27.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:27.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:27.821][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:27.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:27.824][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.824][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.825][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.826][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.830][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:27.830][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:27.831][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.832][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.833][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:27.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:27.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.835][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:27.836][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:27.837][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.838][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.839][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:27.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:27.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.842][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:27.842][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:27.843][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.844][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:27.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:27.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.848][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:27.848][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:27.849][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.850][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:27.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:27.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.854][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:27.855][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:27.856][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.856][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.857][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:27.858][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.859][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.859][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.860][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:27.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.863][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:27.864][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:27.865][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.865][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:27.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:27.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.869][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:27.870][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:27.870][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.871][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:27.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:27.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.875][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:27.885][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:27.886][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.886][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.887][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:27.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:27.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.890][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:27.891][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:27.891][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.892][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:27.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:27.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:27.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:27.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:27.923][self$createEntryFromContent] Accession numbers: 197612. biodb.TRACE[2024-06-29 16:02:27.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:27.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:27.933][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:27.934][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:27.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:27.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:27.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:27.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:27.941][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:27.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:27.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.948][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:27.949][private$selectFields] biodb.TRACE[2024-06-29 16:02:27.950][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:27.950][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:27.951][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:27.952][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.953][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.953][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.954][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.955][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.956][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.956][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.957][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.958][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:27.958][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:27.959][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.960][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.960][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.961][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.962][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:27.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.972][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-06-29 16:02:27.972][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:27.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:27.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:27.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:27.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:27.980][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:27.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:27.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.987][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:27.987][private$selectFields] biodb.TRACE[2024-06-29 16:02:27.988][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:27.989][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:27.990][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:27.990][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.991][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.992][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.993][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.994][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.994][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.995][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:27.996][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:27.997][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:27.997][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:27.998][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:27.999][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.000][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.001][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.001][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:28.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.011][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-06-29 16:02:28.012][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:28.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:28.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:28.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:28.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:28.019][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:28.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:28.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.027][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.027][private$selectFields] biodb.TRACE[2024-06-29 16:02:28.028][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:28.029][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:28.030][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.030][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.031][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.032][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.032][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.033][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.034][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.035][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.035][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.036][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.037][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.037][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.038][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.039][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.040][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.041][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:28.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.051][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-06-29 16:02:28.051][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:28.052][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-06-29 16:02:28.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:28.138][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:28.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:28.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:28.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:28.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:28.145][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:28.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:28.147][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:28.150][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:28.151][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-06-29 16:02:28.152][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:28.154][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-06-29 16:02:28.156][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:28.158][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:28.159][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-06-29 16:02:28.160][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:28.161][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-06-29 16:02:28.163][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:28.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:28.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:28.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:28.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:28.169][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:28.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:28.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:28.179][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:28.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:28.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:28.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:28.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:28.186][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:28.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:28.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:28.196][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:28.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:28.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:28.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:28.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:28.203][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:28.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:28.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:28.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:28.213][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:28.214][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:28.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:28.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:28.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:28.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:28.221][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:28.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:28.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.228][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.229][private$selectFields] biodb.TRACE[2024-06-29 16:02:28.230][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:28.230][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:28.231][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.232][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.232][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.233][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.234][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.234][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.235][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.236][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.237][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.237][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.238][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.239][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.239][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.240][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.241][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.242][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:28.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.251][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-06-29 16:02:28.252][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:28.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:28.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:28.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:28.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:28.259][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:28.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:28.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.290][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.291][private$selectFields] biodb.TRACE[2024-06-29 16:02:28.292][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:28.292][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:28.293][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.294][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.294][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.295][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.296][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.296][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.297][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.298][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.299][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.299][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.306][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.307][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.308][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.308][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.309][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.310][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:28.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.319][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:02:28.320][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:28.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:28.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:28.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:28.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:28.327][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:28.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:28.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.334][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.335][private$selectFields] biodb.TRACE[2024-06-29 16:02:28.335][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:28.336][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:28.337][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.337][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.338][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.339][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.339][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.340][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.341][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.342][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.342][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.343][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.344][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:28.344][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.345][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.346][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.346][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.347][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:28.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:28.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:28.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:28.357][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-06-29 16:02:28.357][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:28.358][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:28.360][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:28.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:28.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:28.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:28.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:28.366][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:28.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:28.374][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:28.376][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:28.377][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:28.378][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:28.716][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:29.053][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:29.055][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content" biodb.TRACE[2024-06-29 16:02:29.058][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.request" biodb.DEBUG[2024-06-29 16:02:29.060][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:29.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:29.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:29.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:29.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:29.067][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:29.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:29.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:29.077][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:29.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:29.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:29.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:29.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:29.083][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:29.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:29.085][private$loadEntries] Creating entries from ids [1]: "91601". biodb.DEBUG[2024-06-29 16:02:29.086][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:29.087][cch$loadFileContent] Trying to load 1 files from cache: [1]: "91601". biodb.TRACE[2024-06-29 16:02:29.088][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:29.088][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:29.089][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:29.090][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:29.090][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:29.091][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:29.093][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:29.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:29.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:29.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:29.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:29.099][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:29.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:29.101][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=91601". biodb.DEBUG[2024-06-29 16:02:29.103][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:29.103][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:29.104][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=91601". biodb.TRACE[2024-06-29 16:02:29.446][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=91601). biodb.DEBUG[2024-06-29 16:02:29.780][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:29.782][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aa7bc0b3048e5fb322307698a3f56fa6.content" biodb.TRACE[2024-06-29 16:02:29.785][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aa7bc0b3048e5fb322307698a3f56fa6.request" biodb.TRACE[2024-06-29 16:02:29.786][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/91601.xml" biodb.DEBUG[2024-06-29 16:02:29.788][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:29.789][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:29.790][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:29.791][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:29.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:29.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:29.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:29.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:29.797][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:29.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:29.800][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:29.800][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:29.801][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.802][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:29.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:29.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.806][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:29.806][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:29.807][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.808][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.808][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:29.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:29.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.811][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:29.812][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:29.813][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.814][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.815][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:29.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:29.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.818][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:29.818][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:29.819][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.820][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:29.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:29.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.823][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:29.824][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:29.825][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.826][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:29.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:29.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.829][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:29.830][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:29.831][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.831][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.832][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:29.833][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:29.834][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.834][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.835][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:29.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:29.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.838][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.839][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.839][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.840][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.844][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:29.845][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:29.845][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.846][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:29.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:29.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.850][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:29.850][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:29.851][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.852][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.853][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:29.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:29.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.856][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:29.856][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:29.857][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.858][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.858][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:29.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:29.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:29.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:29.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:29.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:29.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:29.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:29.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:29.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:29.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:29.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:29.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:29.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:29.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:29.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:29.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:29.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:29.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:29.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:29.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:29.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:29.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:29.891][self$createEntryFromContent] Accession numbers: 91601. biodb.TRACE[2024-06-29 16:02:29.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:29.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:29.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:29.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:29.901][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:29.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:29.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:29.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:29.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:29.908][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:29.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:29.909][private$loadEntries] Creating entries from ids [1]: "95147". biodb.DEBUG[2024-06-29 16:02:29.910][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:29.911][cch$loadFileContent] Trying to load 1 files from cache: [1]: "95147". biodb.TRACE[2024-06-29 16:02:29.912][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:29.913][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:29.914][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:29.914][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:29.915][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:29.916][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:29.918][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:29.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:29.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:29.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:29.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:29.924][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:29.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:29.926][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=95147". biodb.DEBUG[2024-06-29 16:02:29.928][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:29.928][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:29.929][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=95147". biodb.TRACE[2024-06-29 16:02:30.269][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=95147). biodb.DEBUG[2024-06-29 16:02:30.603][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:30.605][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d5dbc153d74635342b8ea0e83790c39e.content" biodb.TRACE[2024-06-29 16:02:30.608][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d5dbc153d74635342b8ea0e83790c39e.request" biodb.TRACE[2024-06-29 16:02:30.610][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/95147.xml" biodb.DEBUG[2024-06-29 16:02:30.611][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:30.612][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:30.613][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:30.614][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:30.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:30.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:30.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:30.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:30.621][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:30.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:30.623][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:30.624][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:30.625][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.626][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:30.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:30.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.630][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:30.631][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:30.632][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.632][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.633][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:30.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:30.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.637][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:30.637][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:30.638][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.639][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.640][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:30.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:30.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.643][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:30.644][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:30.645][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.650][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:30.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:30.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.662][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:30.663][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:30.664][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.664][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:30.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:30.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.668][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:30.669][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:30.670][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.671][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.672][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:30.673][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:30.673][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.674][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.675][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:30.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:30.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.678][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:30.678][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:30.679][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.680][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:30.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:30.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.684][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:30.685][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:30.685][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.686][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:30.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:30.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.691][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:30.691][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:30.692][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.693][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.694][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:30.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:30.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.697][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:30.698][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:30.698][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.699][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.700][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:30.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:30.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:30.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:30.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:30.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:30.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:30.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:30.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:30.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:30.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:30.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:30.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:30.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:30.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:30.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:30.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:30.732][self$createEntryFromContent] Accession numbers: 95147. biodb.TRACE[2024-06-29 16:02:30.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:30.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:30.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:30.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:30.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:30.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:30.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:30.742][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:30.743][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:30.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:30.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:30.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:30.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:30.750][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:30.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:30.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.758][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.759][private$selectFields] biodb.TRACE[2024-06-29 16:02:30.760][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:30.760][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:30.761][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.762][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.763][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.764][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.764][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.765][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.766][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.766][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.767][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.768][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.769][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.770][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.770][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.771][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.772][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.772][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:30.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.782][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:02:30.783][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:30.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:30.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:30.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:30.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:30.791][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:30.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:30.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.798][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.799][private$selectFields] biodb.TRACE[2024-06-29 16:02:30.800][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:30.801][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:30.801][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.802][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.803][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.804][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.804][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.805][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.806][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.807][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.807][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.808][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.809][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.809][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.810][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.811][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.812][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.812][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:30.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.823][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-06-29 16:02:30.824][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:30.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:30.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:30.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:30.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:30.831][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:30.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:30.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.839][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.840][private$selectFields] biodb.TRACE[2024-06-29 16:02:30.841][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:30.842][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:30.842][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.843][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.844][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.845][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.845][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.846][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.847][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.848][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.848][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.849][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.850][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:30.851][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.851][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.852][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.853][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.854][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:30.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:30.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:30.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:30.864][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-06-29 16:02:30.865][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:30.866][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:30.867][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:30.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:30.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:30.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:30.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:30.875][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:30.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:30.877][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:30.880][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:30.881][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:30.882][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:31.218][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:31.556][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:31.558][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content" biodb.TRACE[2024-06-29 16:02:31.561][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.request" biodb.DEBUG[2024-06-29 16:02:31.563][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:31.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:31.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:31.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:31.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:31.570][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:31.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:31.572][private$loadEntries] Creating entries from ids [1]: "636". biodb.DEBUG[2024-06-29 16:02:31.572][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:31.573][cch$loadFileContent] Trying to load 1 files from cache: [1]: "636". biodb.TRACE[2024-06-29 16:02:31.574][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:31.575][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:31.576][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:31.576][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:31.577][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:31.578][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:31.580][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:31.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:31.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:31.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:31.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:31.587][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:31.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:31.588][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=636". biodb.DEBUG[2024-06-29 16:02:31.599][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:31.602][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:31.604][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=636". biodb.TRACE[2024-06-29 16:02:31.949][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=636). biodb.DEBUG[2024-06-29 16:02:32.295][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:32.296][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ccb008951a89970d7f0e2dfe6ae3860d.content" biodb.TRACE[2024-06-29 16:02:32.299][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ccb008951a89970d7f0e2dfe6ae3860d.request" biodb.TRACE[2024-06-29 16:02:32.301][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/636.xml" biodb.DEBUG[2024-06-29 16:02:32.302][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:32.303][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:32.303][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:32.305][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:32.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:32.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:32.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:32.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:32.311][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:32.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:32.313][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:32.314][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:32.315][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.315][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:32.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:32.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.319][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:32.320][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:32.320][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.321][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.322][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:32.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:32.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.325][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:32.325][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:32.326][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.327][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:32.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:32.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.330][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:32.331][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:32.332][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.332][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:32.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:32.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.336][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:32.337][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:32.337][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.338][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.339][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:32.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:32.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.341][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:32.342][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:32.343][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.343][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.344][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:32.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:32.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.347][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:32.348][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:32.348][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.349][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.350][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:32.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:32.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.353][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:32.353][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:32.354][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.354][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:32.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:32.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.358][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:32.359][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:32.359][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.360][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:32.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:32.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.364][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:32.365][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:32.365][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.366][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.367][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:32.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:32.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.370][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:32.371][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:32.371][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.372][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.373][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:32.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:32.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:32.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:32.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:32.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:32.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:32.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:32.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:32.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:32.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:32.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:32.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:32.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:32.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:32.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:32.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:32.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:32.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:32.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:32.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:32.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:32.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:32.404][self$createEntryFromContent] Accession numbers: 636. biodb.TRACE[2024-06-29 16:02:32.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:32.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:32.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:32.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:32.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:32.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:32.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:32.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:32.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:32.414][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:32.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:32.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:32.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:32.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:32.421][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:32.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:32.423][private$loadEntries] Creating entries from ids [1]: "64199". biodb.DEBUG[2024-06-29 16:02:32.424][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:32.425][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64199". biodb.TRACE[2024-06-29 16:02:32.426][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:32.427][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:32.428][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:32.428][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:32.429][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:32.430][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:32.432][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:32.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:32.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:32.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:32.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:32.438][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:32.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:32.440][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64199". biodb.DEBUG[2024-06-29 16:02:32.442][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:32.443][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:32.444][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64199". biodb.TRACE[2024-06-29 16:02:32.786][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64199). biodb.DEBUG[2024-06-29 16:02:33.124][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:33.125][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a31cc2b07404761abdda19d4ffeaa880.content" biodb.TRACE[2024-06-29 16:02:33.128][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a31cc2b07404761abdda19d4ffeaa880.request" biodb.TRACE[2024-06-29 16:02:33.130][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64199.xml" biodb.DEBUG[2024-06-29 16:02:33.132][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:33.133][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:33.134][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:33.135][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:33.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:33.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:33.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:33.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:33.142][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:33.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:33.145][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:33.146][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:33.146][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.147][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:33.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:33.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.152][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:33.153][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:33.153][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.154][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.155][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:33.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:33.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.158][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:33.159][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:33.160][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.160][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.161][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:33.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:33.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.165][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:33.165][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:33.166][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.167][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:33.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:33.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.171][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:33.172][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:33.173][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.173][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:33.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:33.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.177][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:33.178][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:33.179][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.180][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.180][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:33.181][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:33.182][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.183][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.184][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:33.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:33.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.187][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:33.188][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:33.188][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.189][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:33.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:33.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.193][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:33.194][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:33.195][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.195][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:33.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:33.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.200][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:33.201][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:33.201][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.202][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.203][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:33.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:33.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.206][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:33.207][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:33.207][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.208][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.209][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:33.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:33.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:33.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:33.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:33.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:33.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:33.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:33.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:33.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:33.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:33.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:33.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:33.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:33.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:33.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:33.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:33.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:33.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:33.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:33.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:33.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:33.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:33.252][self$createEntryFromContent] Accession numbers: 64199. biodb.TRACE[2024-06-29 16:02:33.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:33.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:33.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:33.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:33.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:33.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:33.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:33.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:33.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:33.262][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:33.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:33.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:33.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:33.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:33.270][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:33.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:33.271][private$loadEntries] Creating entries from ids [1]: "65648". biodb.DEBUG[2024-06-29 16:02:33.272][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:33.273][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65648". biodb.TRACE[2024-06-29 16:02:33.274][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:33.275][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:33.276][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:33.277][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:33.278][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:33.278][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:33.280][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:33.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:33.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:33.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:33.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:33.287][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:33.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:33.289][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65648". biodb.DEBUG[2024-06-29 16:02:33.291][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:33.292][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:33.293][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65648". biodb.TRACE[2024-06-29 16:02:33.637][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65648). biodb.DEBUG[2024-06-29 16:02:33.979][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:33.980][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4176d017d73a3b7cdd77f889aa9b1b1d.content" biodb.TRACE[2024-06-29 16:02:33.983][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4176d017d73a3b7cdd77f889aa9b1b1d.request" biodb.TRACE[2024-06-29 16:02:33.985][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65648.xml" biodb.DEBUG[2024-06-29 16:02:33.986][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:33.987][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:33.988][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:33.990][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:33.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:33.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:33.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:33.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:33.997][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:33.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.000][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:34.001][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:34.001][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.002][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:34.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:34.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.006][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:34.007][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:34.007][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.008][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.009][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:34.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:34.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.012][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:34.013][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:34.013][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.014][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.015][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:34.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:34.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.019][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:34.019][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:34.020][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.021][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:34.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:34.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.025][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:34.026][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:34.027][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.027][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:34.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:34.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.032][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:34.032][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:34.033][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.034][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.035][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:34.036][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.036][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.037][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.038][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:34.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.041][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:34.042][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:34.043][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.044][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:34.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:34.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.048][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:34.049][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:34.049][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.050][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:34.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:34.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.055][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:34.055][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:34.056][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.057][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.058][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:34.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:34.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.061][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:34.062][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:34.063][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.063][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.064][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:34.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:34.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:34.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:34.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:34.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:34.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:34.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:34.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:34.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:34.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:34.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:34.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:34.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:34.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:34.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:34.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.100][self$createEntryFromContent] Accession numbers: 65648. biodb.TRACE[2024-06-29 16:02:34.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:34.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:34.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:34.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:34.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:34.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:34.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.111][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:34.112][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.119][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.127][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.128][private$selectFields] biodb.TRACE[2024-06-29 16:02:34.129][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:34.129][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:34.130][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.131][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.132][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.133][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.133][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.134][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.135][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.136][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.136][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.137][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.138][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.139][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.140][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.140][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.141][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.142][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:34.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.153][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-06-29 16:02:34.153][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.161][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.169][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.169][private$selectFields] biodb.TRACE[2024-06-29 16:02:34.170][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:34.171][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:34.172][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.172][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.173][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.174][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.175][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.175][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.176][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.177][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.178][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.178][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.179][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.180][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.181][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.181][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.182][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.183][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:34.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.201][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [64199]. biodb.DEBUG[2024-06-29 16:02:34.202][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.210][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.218][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.218][private$selectFields] biodb.TRACE[2024-06-29 16:02:34.219][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:34.220][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:34.220][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.221][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.222][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.223][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.224][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.224][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.225][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.226][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.227][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.227][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.228][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.229][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.230][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.230][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.231][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.232][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:34.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.243][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65648]. biodb.DEBUG[2024-06-29 16:02:34.243][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:34.244][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-06-29 16:02:34.251][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:02:34.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:02:34.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.255][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:02:34.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:02:34.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.257][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:02:34.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:02:34.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-29 16:02:34.263][biodb::testThat] biodb.INFO [2024-06-29 16:02:34.264][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() "). biodb.INFO [2024-06-29 16:02:34.265][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:02:34.265][biodb::testThat] biodb.TRACE[2024-06-29 16:02:34.267][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:34.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:34.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.270][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:34.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:34.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.274][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:34.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:34.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.317][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.324][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:34.327][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:34.330][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:34.331][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-06-29 16:02:34.332][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:34.333][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-06-29 16:02:34.335][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.342][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.354][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:34.357][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:34.358][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-06-29 16:02:34.359][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:34.360][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-06-29 16:02:34.362][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.369][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.380][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.387][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.399][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:34.400][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.407][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.415][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.416][private$selectFields] biodb.TRACE[2024-06-29 16:02:34.417][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:34.417][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:34.418][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.419][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.420][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.420][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.421][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.422][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.423][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.423][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.424][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.425][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.426][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.426][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.427][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.428][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.429][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.429][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:34.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.440][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2024-06-29 16:02:34.441][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.448][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.456][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.457][private$selectFields] biodb.TRACE[2024-06-29 16:02:34.458][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:34.458][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:34.459][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.460][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.461][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.461][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.462][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.463][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.464][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.465][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.466][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.466][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.467][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.468][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.469][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.469][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.470][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.471][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:34.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.486][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:02:34.487][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.494][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.502][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.503][private$selectFields] biodb.TRACE[2024-06-29 16:02:34.504][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:34.505][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:34.506][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.506][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.507][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.508][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.509][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.509][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.510][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.511][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.511][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.512][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.513][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.514][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.514][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.515][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.516][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.516][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:34.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.526][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2024-06-29 16:02:34.527][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:34.528][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:34.529][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.536][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:34.539][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:34.542][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:34.543][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-06-29 16:02:34.544][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:34.545][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-06-29 16:02:34.546][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.554][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.565][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.572][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.584][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:34.587][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:34.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-06-29 16:02:34.589][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:34.590][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-06-29 16:02:34.592][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.599][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.610][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.617][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.628][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.635][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.645][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:34.646][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.653][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.660][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.661][private$selectFields] biodb.TRACE[2024-06-29 16:02:34.661][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:34.662][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:34.663][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.664][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.664][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.665][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.666][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.667][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.667][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.668][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.669][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.669][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.670][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.671][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.672][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.672][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.673][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.674][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:34.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.684][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:02:34.684][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.691][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.699][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.700][private$selectFields] biodb.TRACE[2024-06-29 16:02:34.700][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:34.701][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:34.702][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.703][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.704][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.704][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.705][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.706][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.706][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.707][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.708][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.708][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.709][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.710][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.711][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.711][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.712][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.713][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:34.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.723][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-06-29 16:02:34.723][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.730][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.738][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.739][private$selectFields] biodb.TRACE[2024-06-29 16:02:34.739][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:34.740][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:34.741][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.742][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.747][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.748][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.749][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.749][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.750][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.751][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.751][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.752][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.753][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:34.754][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.754][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.755][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.756][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.756][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:34.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:34.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.765][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-06-29 16:02:34.766][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:34.767][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:34.768][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.775][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:34.778][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:34.780][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:34.781][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-06-29 16:02:34.781][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:34.782][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-06-29 16:02:34.785][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.791][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.801][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.808][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.818][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:34.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:34.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:34.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:34.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:34.825][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:34.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:34.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:34.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:34.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:34.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:34.836][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.4*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:34.839][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:34.840][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:34.841][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.4%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:35.192][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.4%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:35.703][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:35.704][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dd9d19fb78fcc7453eff2e9dd7ba5702.content" biodb.TRACE[2024-06-29 16:02:35.707][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dd9d19fb78fcc7453eff2e9dd7ba5702.request" biodb.DEBUG[2024-06-29 16:02:35.712][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:35.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:35.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:35.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:35.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:35.719][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:35.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:35.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:35.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:35.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:35.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:35.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:35.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:35.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:35.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:35.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:35.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:35.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:35.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:35.729][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:35.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:35.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:35.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:35.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:35.736][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:35.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:35.737][private$loadEntries] Creating entries from ids [1]: "3017". biodb.DEBUG[2024-06-29 16:02:35.738][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:35.739][cch$loadFileContent] Trying to load 1 files from cache: [1]: "3017". biodb.TRACE[2024-06-29 16:02:35.740][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:35.741][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:35.742][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:35.742][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:35.743][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:35.744][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:35.746][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:35.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:35.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:35.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:35.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:35.752][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:35.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:35.754][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3017". biodb.DEBUG[2024-06-29 16:02:35.756][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:35.757][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:35.758][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3017". biodb.TRACE[2024-06-29 16:02:36.109][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3017). biodb.DEBUG[2024-06-29 16:02:36.448][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:36.450][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a0d2dadbafdef2154bb32b0db7e287ac.content" biodb.TRACE[2024-06-29 16:02:36.452][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a0d2dadbafdef2154bb32b0db7e287ac.request" biodb.TRACE[2024-06-29 16:02:36.454][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3017.xml" biodb.DEBUG[2024-06-29 16:02:36.455][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:36.456][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:36.457][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:36.458][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:36.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:36.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:36.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:36.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:36.465][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:36.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:36.467][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:36.468][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:36.468][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.469][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:36.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:36.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.473][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:36.474][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:36.474][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.475][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.476][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:36.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:36.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.479][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:36.479][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:36.480][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.481][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.482][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:36.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:36.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.485][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:36.486][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:36.487][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.487][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:36.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:36.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.491][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:36.492][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:36.493][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.493][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:36.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:36.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.497][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:36.498][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:36.499][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.499][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.500][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:36.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:36.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.503][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:36.504][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:36.505][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.505][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.506][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:36.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:36.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.509][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:36.510][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:36.511][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.512][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:36.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:36.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.516][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:36.516][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:36.517][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.518][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:36.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:36.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.522][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:36.523][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:36.523][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.524][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.525][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:36.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:36.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.528][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:36.529][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:36.530][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.530][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.531][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:36.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:36.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:36.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:36.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:36.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:36.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:36.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:36.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:36.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:36.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:36.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:36.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:36.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:36.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:36.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:36.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:36.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:36.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:36.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:36.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:36.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:36.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:36.573][self$createEntryFromContent] Accession numbers: 3017. biodb.TRACE[2024-06-29 16:02:36.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:36.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:36.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:36.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:36.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:36.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:36.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:36.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:36.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:36.582][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:36.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:36.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:36.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:36.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:36.589][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:36.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:36.590][private$loadEntries] Creating entries from ids [1]: "3510". biodb.DEBUG[2024-06-29 16:02:36.591][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:36.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "3510". biodb.TRACE[2024-06-29 16:02:36.593][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:36.594][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:36.594][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:36.595][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:36.596][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:36.597][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:36.599][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:36.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:36.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:36.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:36.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:36.605][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:36.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:36.607][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3510". biodb.DEBUG[2024-06-29 16:02:36.609][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:36.609][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:36.610][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3510". biodb.TRACE[2024-06-29 16:02:36.961][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3510). biodb.DEBUG[2024-06-29 16:02:37.319][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:37.320][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/58362fa70b44eecb6a87afbf9b6dfd8b.content" biodb.TRACE[2024-06-29 16:02:37.323][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/58362fa70b44eecb6a87afbf9b6dfd8b.request" biodb.TRACE[2024-06-29 16:02:37.325][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3510.xml" biodb.DEBUG[2024-06-29 16:02:37.326][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:37.327][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:37.328][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:37.329][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:37.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:37.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:37.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:37.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:37.336][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:37.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:37.338][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:37.339][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:37.340][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.341][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:37.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:37.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.344][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:37.345][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:37.346][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.346][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.347][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:37.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:37.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.350][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:37.351][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:37.352][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.353][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.354][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:37.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:37.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.357][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:37.358][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:37.359][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.359][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:37.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:37.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.363][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:37.364][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:37.365][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.365][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:37.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:37.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.369][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:37.370][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:37.371][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.371][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.372][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:37.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:37.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.375][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:37.376][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:37.377][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.377][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.378][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:37.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:37.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.381][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:37.382][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:37.383][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.383][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:37.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:37.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.387][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:37.388][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:37.389][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.389][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.390][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:37.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:37.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.393][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:37.394][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:37.395][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.395][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.396][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:37.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:37.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.399][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:37.400][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:37.401][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.401][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.402][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:37.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:37.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:37.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:37.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:37.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:37.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:37.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:37.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:37.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:37.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:37.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:37.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:37.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:37.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:37.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:37.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:37.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:37.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:37.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:37.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:37.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:37.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:37.435][self$createEntryFromContent] Accession numbers: 3510. biodb.TRACE[2024-06-29 16:02:37.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:37.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:37.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:37.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:37.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:37.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:37.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:37.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:37.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:37.445][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:37.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:37.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:37.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:37.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:37.452][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:37.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:37.453][private$loadEntries] Creating entries from ids [1]: "7554". biodb.DEBUG[2024-06-29 16:02:37.454][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:37.455][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7554". biodb.TRACE[2024-06-29 16:02:37.456][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:37.457][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:37.457][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:37.458][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:37.459][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:37.460][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:37.461][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:37.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:37.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:37.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:37.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:37.468][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:37.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:37.470][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7554". biodb.DEBUG[2024-06-29 16:02:37.472][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:37.473][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:37.474][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7554". biodb.TRACE[2024-06-29 16:02:37.813][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7554). biodb.DEBUG[2024-06-29 16:02:38.148][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:38.150][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66bd6c2472b2485e58ad424b4505cbea.content" biodb.TRACE[2024-06-29 16:02:38.153][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66bd6c2472b2485e58ad424b4505cbea.request" biodb.TRACE[2024-06-29 16:02:38.154][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7554.xml" biodb.DEBUG[2024-06-29 16:02:38.156][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:38.157][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:38.158][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:38.159][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.166][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:38.168][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:38.169][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:38.169][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.170][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:38.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:38.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.174][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:38.175][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:38.176][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.176][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.177][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:38.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:38.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.180][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:38.181][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:38.181][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.182][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.183][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:38.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:38.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.186][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:38.187][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:38.187][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.188][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.189][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:38.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:38.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.192][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:38.193][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:38.202][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.203][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:38.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:38.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.207][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:38.208][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:38.208][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.209][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.210][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:38.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:38.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.213][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:38.213][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:38.214][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.215][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.216][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:38.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:38.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.218][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.219][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.220][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.220][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.224][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:38.225][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:38.226][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.226][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:38.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:38.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.230][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:38.231][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:38.231][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.232][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.233][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:38.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:38.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.236][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:38.237][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:38.237][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.238][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.239][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:38.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:38.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:38.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:38.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:38.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:38.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:38.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:38.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:38.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:38.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:38.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:38.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:38.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:38.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:38.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:38.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:38.270][self$createEntryFromContent] Accession numbers: 7554. biodb.TRACE[2024-06-29 16:02:38.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:38.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:38.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:38.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:38.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:38.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:38.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:38.280][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:38.281][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.288][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:38.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.296][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.297][private$selectFields] biodb.TRACE[2024-06-29 16:02:38.297][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:38.298][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:38.299][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.300][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.300][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.301][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.302][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.303][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.304][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.304][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.305][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.306][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.307][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.308][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.309][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.309][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.310][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.311][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:38.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.321][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-06-29 16:02:38.322][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.329][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:38.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.337][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.338][private$selectFields] biodb.TRACE[2024-06-29 16:02:38.338][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:38.339][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:38.340][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.341][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.341][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.342][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.343][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.343][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.344][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.345][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.346][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.346][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.347][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.348][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.348][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.349][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.350][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.351][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:38.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.361][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3017]. biodb.DEBUG[2024-06-29 16:02:38.362][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.369][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:38.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.376][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.377][private$selectFields] biodb.TRACE[2024-06-29 16:02:38.378][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:38.378][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:38.379][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.380][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.380][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.381][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.382][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.382][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.383][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.384][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.384][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.385][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.386][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.387][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.387][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.388][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.389][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.390][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:38.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.399][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7554]. biodb.DEBUG[2024-06-29 16:02:38.400][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:38.401][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-06-29 16:02:38.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:38.445][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.452][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:38.459][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:38.461][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:38.462][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-06-29 16:02:38.463][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:38.464][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-06-29 16:02:38.467][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:38.469][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:38.470][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-06-29 16:02:38.470][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:38.471][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-06-29 16:02:38.473][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.480][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:38.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:38.490][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.497][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:38.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:38.507][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.514][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:38.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:38.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:38.524][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:38.525][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.532][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:38.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.539][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.540][private$selectFields] biodb.TRACE[2024-06-29 16:02:38.540][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:38.541][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:38.542][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.542][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.543][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.544][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.545][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.545][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.546][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.547][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.547][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.548][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.549][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.550][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.551][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.552][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.552][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.553][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:38.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.564][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-06-29 16:02:38.564][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.571][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:38.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.579][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.580][private$selectFields] biodb.TRACE[2024-06-29 16:02:38.580][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:38.581][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:38.582][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.582][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.583][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.584][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.584][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.585][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.586][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.587][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.587][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.588][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.589][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.589][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.590][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.591][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.592][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.592][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:38.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.602][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:02:38.603][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.610][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:38.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.618][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.619][private$selectFields] biodb.TRACE[2024-06-29 16:02:38.619][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:38.620][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:38.621][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.621][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.622][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.623][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.624][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.624][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.625][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.626][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.626][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.627][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.628][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:38.628][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.629][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.630][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.631][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.631][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:38.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:38.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:38.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:38.641][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-06-29 16:02:38.642][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:38.643][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:38.644][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:38.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:38.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:38.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:38.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:38.651][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:38.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:38.654][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.3*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:38.656][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:38.657][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:38.658][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.3%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:38.998][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.3%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:39.335][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:39.336][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f88afce5e7bcb0842d474b04c0bef37a.content" biodb.TRACE[2024-06-29 16:02:39.340][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f88afce5e7bcb0842d474b04c0bef37a.request" biodb.DEBUG[2024-06-29 16:02:39.342][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:39.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:39.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:39.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:39.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:39.349][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:39.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:39.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:39.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:39.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:39.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:39.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:39.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:39.359][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:39.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:39.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:39.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:39.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:39.366][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:39.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:39.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:39.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:39.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:39.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:39.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:39.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:39.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:39.376][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:39.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:39.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:39.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:39.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:39.383][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:39.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:39.384][private$loadEntries] Creating entries from ids [1]: "27495". biodb.DEBUG[2024-06-29 16:02:39.385][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:39.386][cch$loadFileContent] Trying to load 1 files from cache: [1]: "27495". biodb.TRACE[2024-06-29 16:02:39.387][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:39.388][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:39.389][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:39.389][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:39.397][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:39.398][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:39.400][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:39.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:39.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:39.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:39.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:39.407][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:39.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:39.408][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=27495". biodb.DEBUG[2024-06-29 16:02:39.410][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:39.411][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:39.412][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=27495". biodb.TRACE[2024-06-29 16:02:39.769][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=27495). biodb.DEBUG[2024-06-29 16:02:40.105][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:40.107][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/edda5d46cbbeda6cad9b4593b6925e01.content" biodb.TRACE[2024-06-29 16:02:40.109][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/edda5d46cbbeda6cad9b4593b6925e01.request" biodb.TRACE[2024-06-29 16:02:40.111][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/27495.xml" biodb.DEBUG[2024-06-29 16:02:40.112][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:40.113][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:40.114][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:40.115][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:40.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:40.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:40.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:40.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:40.123][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:40.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:40.125][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:40.126][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:40.126][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.127][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:40.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:40.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.131][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:40.131][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:40.132][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.133][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.134][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:40.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:40.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.137][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:40.137][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:40.138][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.139][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.140][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:40.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:40.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.143][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:40.144][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:40.144][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.145][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.146][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:40.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:40.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.149][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:40.150][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:40.150][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.151][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.152][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:40.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:40.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.155][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:40.156][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:40.157][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.157][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.158][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:40.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:40.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.161][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:40.162][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:40.163][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.164][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.165][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:40.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:40.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.167][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.168][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.169][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.169][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.173][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:40.174][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:40.175][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.175][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.176][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:40.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:40.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.179][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:40.180][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:40.181][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.182][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.183][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:40.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:40.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.186][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:40.186][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:40.187][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.188][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.189][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:40.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:40.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:40.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:40.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.203][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:40.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:40.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:40.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:40.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:40.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:40.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:40.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:40.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:40.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:40.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:40.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:40.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:40.221][self$createEntryFromContent] Accession numbers: 27495. biodb.TRACE[2024-06-29 16:02:40.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:40.231][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:40.232][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:40.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:40.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:40.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:40.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:40.239][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:40.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:40.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.247][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.247][private$selectFields] biodb.TRACE[2024-06-29 16:02:40.248][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:40.249][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:40.249][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.250][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.251][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.251][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.252][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.253][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.253][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.254][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.255][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.256][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.256][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.257][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.258][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.259][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.259][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.260][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:40.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.270][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-06-29 16:02:40.271][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:40.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:40.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:40.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:40.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:40.278][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:40.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:40.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.286][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.286][private$selectFields] biodb.TRACE[2024-06-29 16:02:40.287][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:40.288][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:40.288][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.289][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.290][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.291][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.292][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.292][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.293][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.294][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.295][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.295][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.296][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.297][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.297][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.298][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.299][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.300][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:40.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.310][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-06-29 16:02:40.311][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:40.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:40.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:40.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:40.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:40.318][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:40.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:40.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.325][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.326][private$selectFields] biodb.TRACE[2024-06-29 16:02:40.326][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:40.327][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:40.328][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.329][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.329][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.330][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.331][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.331][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.332][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.333][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.333][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.334][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.335][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:40.336][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.336][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.337][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.338][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.338][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:40.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:40.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.355][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [27495]. biodb.DEBUG[2024-06-29 16:02:40.356][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:40.357][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:40.358][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:40.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:40.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:40.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:40.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:40.365][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:40.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:40.368][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:40.370][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:40.371][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-06-29 16:02:40.372][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:40.373][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-06-29 16:02:40.375][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:40.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:40.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:40.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:40.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:40.381][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:40.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:40.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:40.392][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:40.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:40.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:40.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:40.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:40.399][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:40.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:40.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:40.409][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:40.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:40.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:40.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:40.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:40.416][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:40.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:40.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:40.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:40.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:40.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:40.426][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:40.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:40.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:40.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:40.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:40.432][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:40.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:40.434][private$loadEntries] Creating entries from ids [1]: "65675". biodb.DEBUG[2024-06-29 16:02:40.434][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:40.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65675". biodb.TRACE[2024-06-29 16:02:40.436][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:40.437][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:40.438][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:40.439][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:40.440][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:40.440][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:40.442][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:40.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:40.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:40.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:40.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:40.449][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:40.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:40.451][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65675". biodb.DEBUG[2024-06-29 16:02:40.453][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:40.454][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:40.455][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65675". biodb.TRACE[2024-06-29 16:02:40.797][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65675). biodb.DEBUG[2024-06-29 16:02:41.129][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:41.131][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5e9eb5601826c5f1539c216fc81b6e57.content" biodb.TRACE[2024-06-29 16:02:41.133][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5e9eb5601826c5f1539c216fc81b6e57.request" biodb.TRACE[2024-06-29 16:02:41.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65675.xml" biodb.DEBUG[2024-06-29 16:02:41.137][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:41.138][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:41.139][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:41.140][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:41.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:41.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:41.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:41.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:41.146][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:41.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:41.149][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:41.150][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:41.150][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.151][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:41.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:41.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.155][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:41.156][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:41.156][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.157][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.158][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:41.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:41.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.161][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:41.162][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:41.162][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.163][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.164][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:41.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:41.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.167][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:41.168][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:41.168][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.169][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:41.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:41.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.173][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:41.174][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:41.174][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.175][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:41.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:41.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.179][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:41.179][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:41.180][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.181][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.182][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:41.182][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:41.183][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.184][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.185][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:41.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:41.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.188][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:41.189][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:41.190][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.190][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:41.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:41.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.194][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:41.195][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:41.195][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.196][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:41.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:41.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.200][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:41.201][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:41.202][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.202][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.203][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:41.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:41.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.206][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:41.207][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:41.208][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.208][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.209][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:41.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:41.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:41.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:41.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:41.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:41.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:41.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:41.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:41.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:41.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:41.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:41.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:41.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:41.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:41.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:41.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:41.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:41.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:41.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:41.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:41.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:41.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:41.242][self$createEntryFromContent] Accession numbers: 65675. biodb.TRACE[2024-06-29 16:02:41.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:41.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:41.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:41.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:41.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:41.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:41.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:41.252][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:41.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:41.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:41.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:41.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:41.258][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:41.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:41.260][private$loadEntries] Creating entries from ids [1]: "66318". biodb.DEBUG[2024-06-29 16:02:41.260][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:41.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66318". biodb.TRACE[2024-06-29 16:02:41.263][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:41.263][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:41.264][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:41.265][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:41.266][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:41.267][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:41.269][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:41.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:41.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:41.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:41.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:41.276][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:41.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:41.284][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66318". biodb.DEBUG[2024-06-29 16:02:41.286][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:41.287][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:41.288][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66318". biodb.TRACE[2024-06-29 16:02:41.628][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66318). biodb.DEBUG[2024-06-29 16:02:41.972][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:41.974][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f7af403e0af2ad309d5e7b7572ad9eab.content" biodb.TRACE[2024-06-29 16:02:41.976][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f7af403e0af2ad309d5e7b7572ad9eab.request" biodb.TRACE[2024-06-29 16:02:41.978][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66318.xml" biodb.DEBUG[2024-06-29 16:02:41.979][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:41.980][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:41.981][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:41.982][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:41.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:41.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:41.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:41.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:41.989][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:41.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:41.991][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:41.992][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:41.993][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.993][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:41.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:41.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:41.997][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:41.998][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:41.999][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:41.999][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.000][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:42.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:42.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.003][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:42.004][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:42.004][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.005][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.006][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:42.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:42.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.009][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:42.010][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:42.010][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.011][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:42.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:42.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.015][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:42.015][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:42.016][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.017][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:42.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:42.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.021][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:42.021][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:42.022][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.023][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.024][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:42.024][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:42.025][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.026][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.027][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:42.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:42.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.029][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.030][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.031][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.031][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.035][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:42.036][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:42.036][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.037][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:42.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:42.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.041][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:42.042][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:42.042][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.043][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.044][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:42.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:42.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.047][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:42.047][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:42.048][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.049][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.050][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:42.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:42.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:42.083][self$createEntryFromContent] Accession numbers: 66318. biodb.TRACE[2024-06-29 16:02:42.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:42.092][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:42.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:42.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:42.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:42.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:42.099][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:42.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:42.101][private$loadEntries] Creating entries from ids [1]: "67547". biodb.DEBUG[2024-06-29 16:02:42.101][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:42.103][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67547". biodb.TRACE[2024-06-29 16:02:42.104][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:42.104][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:42.105][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:42.106][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:42.107][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:42.108][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:42.110][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:42.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:42.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:42.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:42.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:42.117][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:42.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:42.118][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67547". biodb.DEBUG[2024-06-29 16:02:42.120][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:42.121][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:42.122][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67547". biodb.TRACE[2024-06-29 16:02:42.468][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67547). biodb.DEBUG[2024-06-29 16:02:42.881][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:42.882][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5dcb6d289b29a3e5a91ef3f664ac8354.content" biodb.TRACE[2024-06-29 16:02:42.885][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5dcb6d289b29a3e5a91ef3f664ac8354.request" biodb.TRACE[2024-06-29 16:02:42.887][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67547.xml" biodb.DEBUG[2024-06-29 16:02:42.888][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:42.889][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:42.890][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:42.891][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:42.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:42.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:42.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:42.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:42.898][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:42.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:42.901][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.902][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.902][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.903][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.907][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:42.908][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:42.909][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.909][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.910][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:42.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:42.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.913][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:42.914][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:42.915][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.915][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.916][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:42.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:42.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.919][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:42.920][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:42.921][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.922][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:42.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:42.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.926][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:42.927][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:42.927][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.928][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:42.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:42.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.932][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:42.932][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:42.933][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.934][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.934][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:42.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:42.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.938][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:42.938][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:42.939][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.940][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.940][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:42.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:42.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.943][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.944][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.945][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.945][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:42.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.949][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:42.950][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:42.950][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.951][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:42.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:42.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.955][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:42.956][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:42.956][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.957][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.958][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:42.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:42.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.961][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:42.962][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:42.963][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.963][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.964][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:42.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:42.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:42.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:42.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:42.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:42.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:42.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:43.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:43.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:43.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:43.004][self$createEntryFromContent] Accession numbers: 67547. biodb.TRACE[2024-06-29 16:02:43.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:43.013][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:43.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:43.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:43.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:43.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:43.020][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:43.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:43.021][private$loadEntries] Creating entries from ids [1]: "69550". biodb.DEBUG[2024-06-29 16:02:43.022][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:43.023][cch$loadFileContent] Trying to load 1 files from cache: [1]: "69550". biodb.TRACE[2024-06-29 16:02:43.024][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:43.025][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:43.025][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:43.026][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:43.027][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:43.028][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:43.030][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:43.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:43.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:43.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:43.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:43.036][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:43.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:43.038][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69550". biodb.DEBUG[2024-06-29 16:02:43.040][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:43.040][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:43.041][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69550". biodb.TRACE[2024-06-29 16:02:43.424][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69550). biodb.DEBUG[2024-06-29 16:02:43.795][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:43.797][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/05703421c7bf99b1d8473c1de6165168.content" biodb.TRACE[2024-06-29 16:02:43.799][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/05703421c7bf99b1d8473c1de6165168.request" biodb.TRACE[2024-06-29 16:02:43.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/69550.xml" biodb.DEBUG[2024-06-29 16:02:43.803][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:43.803][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:43.804][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:43.805][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:43.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:43.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:43.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:43.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:43.812][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:43.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:43.814][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:43.815][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:43.816][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.816][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:43.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:43.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.820][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:43.821][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:43.822][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.822][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.823][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:43.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:43.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.827][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:43.827][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:43.828][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.829][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.830][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:43.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:43.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.833][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:43.833][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:43.834][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.835][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.836][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:43.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:43.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.839][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:43.839][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:43.840][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.841][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.842][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:43.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:43.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.844][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:43.845][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:43.846][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.847][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.848][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:43.848][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:43.849][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.850][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.851][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:43.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:43.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.853][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.854][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.855][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.856][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.860][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:43.860][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:43.861][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.862][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:43.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:43.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.866][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:43.867][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:43.867][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.868][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.869][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:43.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:43.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.872][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:43.873][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:43.874][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.874][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.875][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:43.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:43.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:43.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:43.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:43.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:43.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:43.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:43.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:43.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:43.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:43.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:43.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:43.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:43.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:43.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:43.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:43.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:43.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:43.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:43.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:43.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:43.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:43.908][self$createEntryFromContent] Accession numbers: 69550. biodb.TRACE[2024-06-29 16:02:43.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:43.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:43.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:43.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:43.918][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:43.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:43.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:43.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:43.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:43.925][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:43.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:43.927][private$loadEntries] Creating entries from ids [1]: "71520". biodb.DEBUG[2024-06-29 16:02:43.927][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:43.929][cch$loadFileContent] Trying to load 1 files from cache: [1]: "71520". biodb.TRACE[2024-06-29 16:02:43.930][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:43.930][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:43.931][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:43.932][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:43.933][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:43.934][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:43.936][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:43.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:43.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:43.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:43.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:43.942][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:43.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:43.944][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71520". biodb.DEBUG[2024-06-29 16:02:43.946][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:43.946][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:43.947][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71520". biodb.TRACE[2024-06-29 16:02:44.304][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71520). biodb.DEBUG[2024-06-29 16:02:44.653][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:44.655][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e7ceab0ba86590faa4ea87df2e390610.content" biodb.TRACE[2024-06-29 16:02:44.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e7ceab0ba86590faa4ea87df2e390610.request" biodb.TRACE[2024-06-29 16:02:44.659][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/71520.xml" biodb.DEBUG[2024-06-29 16:02:44.661][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:44.661][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:44.662][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:44.664][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:44.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:44.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:44.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:44.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:44.670][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:44.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:44.673][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:44.674][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:44.674][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.675][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:44.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:44.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.679][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:44.680][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:44.680][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.681][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.682][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:44.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:44.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.685][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:44.686][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:44.687][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.687][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.688][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:44.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:44.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.701][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:44.702][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:44.703][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.703][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:44.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:44.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.707][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:44.708][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:44.709][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.709][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:44.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:44.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.713][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:44.714][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:44.715][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.715][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.716][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:44.717][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:44.718][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.718][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.719][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:44.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:44.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.722][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:44.723][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:44.724][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.724][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:44.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:44.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.728][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:44.729][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:44.730][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.731][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:44.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:44.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.734][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:44.735][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:44.736][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.736][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.737][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:44.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:44.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.740][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:44.741][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:44.742][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.742][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.743][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:44.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:44.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:44.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:44.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:44.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:44.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:44.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:44.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:44.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:44.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:44.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:44.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:44.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:44.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:44.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:44.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:44.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:44.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:44.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:44.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:44.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:44.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:44.775][self$createEntryFromContent] Accession numbers: 71520. biodb.TRACE[2024-06-29 16:02:44.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:44.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:44.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:44.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:44.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:44.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:44.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:44.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:44.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:44.785][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:44.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:44.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:44.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:44.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:44.792][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:44.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:44.793][private$loadEntries] Creating entries from ids [1]: "77600". biodb.DEBUG[2024-06-29 16:02:44.794][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:44.795][cch$loadFileContent] Trying to load 1 files from cache: [1]: "77600". biodb.TRACE[2024-06-29 16:02:44.796][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:44.797][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:44.798][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:44.799][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:44.799][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:44.800][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:44.802][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:44.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:44.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:44.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:44.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:44.809][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:44.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:44.811][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77600". biodb.DEBUG[2024-06-29 16:02:44.813][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:44.814][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:44.815][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77600". biodb.TRACE[2024-06-29 16:02:45.157][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77600). biodb.DEBUG[2024-06-29 16:02:45.492][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:45.494][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/91aa415bb91d90afd912e94b5d252faa.content" biodb.TRACE[2024-06-29 16:02:45.497][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/91aa415bb91d90afd912e94b5d252faa.request" biodb.TRACE[2024-06-29 16:02:45.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/77600.xml" biodb.DEBUG[2024-06-29 16:02:45.500][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:45.501][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:45.502][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:45.503][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:45.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:45.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:45.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:45.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:45.510][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:45.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:45.513][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:45.514][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:45.514][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.515][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:45.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:45.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.519][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:45.520][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:45.521][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.521][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.522][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:45.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:45.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.525][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:45.526][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:45.527][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.528][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.528][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:45.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:45.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.531][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:45.532][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:45.533][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.534][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.535][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:45.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:45.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.538][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:45.538][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:45.539][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.540][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:45.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:45.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.543][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:45.544][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:45.545][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.546][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.547][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:45.548][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:45.548][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.549][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.550][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:45.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:45.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.553][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:45.554][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:45.554][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.555][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:45.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:45.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.559][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:45.560][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:45.560][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.561][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:45.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:45.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.565][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:45.566][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:45.567][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.567][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.568][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:45.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:45.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.571][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:45.572][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:45.573][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.573][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.574][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:45.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:45.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:45.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:45.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:45.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:45.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:45.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:45.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:45.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:45.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:45.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:45.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:45.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:45.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:45.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:45.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:45.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:45.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:45.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:45.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:45.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:45.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:45.606][self$createEntryFromContent] Accession numbers: 77600. biodb.TRACE[2024-06-29 16:02:45.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:45.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:45.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:45.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:45.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:45.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:45.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:45.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:45.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:45.616][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:45.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:45.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:45.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:45.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:45.623][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:45.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:45.625][private$loadEntries] Creating entries from ids [1]: "77601". biodb.DEBUG[2024-06-29 16:02:45.625][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:45.631][cch$loadFileContent] Trying to load 1 files from cache: [1]: "77601". biodb.TRACE[2024-06-29 16:02:45.634][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:45.635][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:45.636][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:45.637][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:45.638][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:45.638][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:45.640][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:45.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:45.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:45.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:45.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:45.647][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:45.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:45.648][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77601". biodb.DEBUG[2024-06-29 16:02:45.650][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:45.651][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:45.652][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77601". biodb.TRACE[2024-06-29 16:02:45.995][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77601). biodb.DEBUG[2024-06-29 16:02:46.331][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:46.333][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ff0e48db0e5117b4127b12d15d1485a8.content" biodb.TRACE[2024-06-29 16:02:46.335][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ff0e48db0e5117b4127b12d15d1485a8.request" biodb.TRACE[2024-06-29 16:02:46.337][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/77601.xml" biodb.DEBUG[2024-06-29 16:02:46.338][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:46.339][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:46.340][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:46.341][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.348][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.350][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:46.351][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:46.352][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.352][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:46.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:46.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.357][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:46.357][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:46.358][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.359][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.360][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:46.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:46.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.362][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:46.363][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:46.364][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.365][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.365][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:46.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:46.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.368][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:46.369][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:46.370][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.371][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:46.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:46.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.374][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:46.375][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:46.376][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.376][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:46.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:46.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.380][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:46.381][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:46.381][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.382][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.383][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:46.384][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.385][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.385][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.386][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:46.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.389][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:46.390][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:46.390][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.391][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:46.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:46.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.395][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:46.396][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:46.396][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.397][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:46.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:46.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.401][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:46.402][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:46.403][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.403][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.404][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:46.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:46.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.407][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:46.408][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:46.409][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.409][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.410][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:46.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:46.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:46.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:46.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:46.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:46.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:46.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:46.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:46.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:46.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:46.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:46.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:46.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:46.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:46.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:46.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:46.443][self$createEntryFromContent] Accession numbers: 77601. biodb.TRACE[2024-06-29 16:02:46.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:46.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:46.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:46.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:46.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:46.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:46.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:46.452][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:46.453][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.461][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.468][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.469][private$selectFields] biodb.TRACE[2024-06-29 16:02:46.469][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:46.470][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:46.471][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.471][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.472][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.473][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.474][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.474][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.475][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.476][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.476][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.477][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.478][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.479][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.479][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.480][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.481][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.481][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:46.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.491][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [64199]. biodb.DEBUG[2024-06-29 16:02:46.492][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.499][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.507][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.508][private$selectFields] biodb.TRACE[2024-06-29 16:02:46.508][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:46.509][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:46.510][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.511][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.511][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.512][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.513][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.513][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.514][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.515][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.516][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.516][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.517][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.518][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.519][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.519][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.520][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.521][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:46.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.530][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [77600]. biodb.DEBUG[2024-06-29 16:02:46.531][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.538][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.545][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.546][private$selectFields] biodb.TRACE[2024-06-29 16:02:46.547][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:46.547][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:46.548][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.549][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.549][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.550][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.551][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.551][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.552][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.553][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.554][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.554][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.555][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.556][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.556][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.557][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.558][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.558][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:46.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.575][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [77601]. biodb.DEBUG[2024-06-29 16:02:46.576][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:46.577][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-06-29 16:02:46.584][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:02:46.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:02:46.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.587][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:02:46.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:02:46.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.589][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:02:46.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:02:46.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-29 16:02:46.595][biodb::testThat] biodb.INFO [2024-06-29 16:02:46.596][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() "). biodb.INFO [2024-06-29 16:02:46.597][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:02:46.597][biodb::testThat] biodb.TRACE[2024-06-29 16:02:46.599][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:46.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:46.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.603][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:46.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:46.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.605][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:46.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:46.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:46.645][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.652][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:46.655][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:46.657][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:46.658][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-06-29 16:02:46.659][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:46.660][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-06-29 16:02:46.662][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.668][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:46.679][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:46.681][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:46.682][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-06-29 16:02:46.683][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:46.684][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-06-29 16:02:46.686][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.693][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:46.703][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.710][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:46.720][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:46.721][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.728][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.735][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.736][private$selectFields] biodb.TRACE[2024-06-29 16:02:46.736][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:46.737][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:46.738][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.739][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.739][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.740][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.741][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.741][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.742][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.743][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.743][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.744][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.745][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.746][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.746][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.747][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.748][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.748][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:46.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.758][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2024-06-29 16:02:46.759][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.766][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.773][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.774][private$selectFields] biodb.TRACE[2024-06-29 16:02:46.774][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:46.775][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:46.776][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.777][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.777][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.778][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.779][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.780][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.780][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.781][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.782][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.782][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.783][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.784][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.785][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.786][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.786][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.787][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:46.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.797][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:02:46.798][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.804][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.812][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.813][private$selectFields] biodb.TRACE[2024-06-29 16:02:46.813][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:46.814][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:46.815][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.816][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.816][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.817][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.818][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.823][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.824][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.825][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.826][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.826][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.827][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.828][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.829][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.829][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.830][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.831][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:46.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.840][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2024-06-29 16:02:46.841][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:46.841][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:46.843][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.850][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:46.852][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:46.854][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:46.855][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-06-29 16:02:46.856][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:46.857][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-06-29 16:02:46.859][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.865][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:46.875][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.882][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:46.892][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:46.895][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:46.896][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-06-29 16:02:46.896][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:46.897][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-06-29 16:02:46.900][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.906][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:46.916][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.923][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:46.933][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.940][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:46.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:46.950][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:46.951][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.958][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.965][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.966][private$selectFields] biodb.TRACE[2024-06-29 16:02:46.966][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:46.967][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:46.968][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.968][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.969][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.970][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.970][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.971][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.972][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.973][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.973][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.974][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.975][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:46.976][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.976][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.977][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.978][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.979][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:46.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:46.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:46.989][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:02:46.989][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:46.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:46.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:46.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:46.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:46.997][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:46.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:46.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:46.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.004][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.005][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.006][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.006][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.007][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.008][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.009][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.009][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.010][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.011][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.012][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.012][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.013][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.014][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.015][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.015][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.016][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.017][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.017][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.018][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.029][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-06-29 16:02:47.029][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.036][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.044][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.044][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.045][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.046][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.047][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.048][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.048][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.049][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.050][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.050][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.051][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.052][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.053][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.053][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.054][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.055][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.055][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.056][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.057][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.058][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.068][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-06-29 16:02:47.069][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:47.070][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:47.071][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.084][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:47.087][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:47.089][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:47.090][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26d0872875c47c33e8205aa7124e0486". biodb.TRACE[2024-06-29 16:02:47.091][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:47.092][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content". biodb.DEBUG[2024-06-29 16:02:47.094][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.101][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.111][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.118][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.129][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.136][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.146][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.152][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.163][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.170][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.180][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.187][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.198][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.204][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.215][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.221][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.232][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:47.234][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:47.235][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-06-29 16:02:47.236][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:47.237][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-06-29 16:02:47.238][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.245][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.255][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.262][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.272][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.279][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:47.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.289][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:47.290][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.297][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.304][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.305][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.305][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.306][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.307][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.307][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.308][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.309][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.309][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.310][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.311][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.312][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.312][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.313][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.314][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.314][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.315][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.316][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.316][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.317][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.327][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-06-29 16:02:47.327][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.334][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.346][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.347][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.348][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.348][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.349][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.350][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.350][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.351][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.352][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.352][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.353][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.354][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.354][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.355][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.356][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.356][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.357][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.358][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.358][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.359][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.368][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-06-29 16:02:47.369][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.376][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.383][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.384][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.384][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.385][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.386][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.386][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.387][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.388][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.388][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.389][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.390][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.391][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.391][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.392][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.393][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.393][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.394][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.395][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.395][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.396][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.406][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-06-29 16:02:47.406][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:47.407][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-06-29 16:02:47.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.463][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.470][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:47.473][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:47.475][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:47.476][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-06-29 16:02:47.477][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:47.478][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-06-29 16:02:47.480][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:47.482][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:47.483][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-06-29 16:02:47.484][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:47.485][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-06-29 16:02:47.487][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.493][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.504][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.511][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.521][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.528][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.538][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:47.539][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.546][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.553][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.554][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.555][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.555][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.556][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.557][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.558][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.559][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.559][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.560][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.561][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.562][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.562][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.563][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.564][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.565][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.565][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.566][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.567][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.567][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.578][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-06-29 16:02:47.579][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.586][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.594][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.594][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.595][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.596][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.601][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.602][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.603][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.604][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.605][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.605][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.606][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.607][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.607][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.608][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.609][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.609][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.610][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.611][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.611][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.612][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.621][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:02:47.622][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.629][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.636][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.637][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.638][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.638][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.639][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.640][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.640][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.641][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.642][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.642][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.643][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.644][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.645][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.645][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.646][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.647][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.647][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.648][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.649][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.649][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.659][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-06-29 16:02:47.659][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:47.660][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:47.662][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.668][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:47.671][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:47.673][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:47.674][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7269bbea581f1e243800f8ee4e0f4fdb". biodb.TRACE[2024-06-29 16:02:47.675][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:47.676][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content". biodb.DEBUG[2024-06-29 16:02:47.678][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.685][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.695][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.702][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.712][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.719][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.729][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:47.730][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.737][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.744][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.745][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.746][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.746][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.747][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.748][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.748][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.749][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.750][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.751][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.752][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.752][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.753][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.754][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.754][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.755][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.756][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.757][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.757][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.758][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.768][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:02:47.768][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.775][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.782][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.783][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.784][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.784][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.785][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.786][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.786][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.787][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.788][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.789][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.789][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.790][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.791][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.791][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.792][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.793][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.793][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.794][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.795][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.795][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.805][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-06-29 16:02:47.806][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.812][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.820][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.820][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.821][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.822][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.822][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.823][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.824][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.824][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.825][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.826][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.827][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.827][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.828][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.829][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.830][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.830][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.831][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.832][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.832][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.833][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.843][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-06-29 16:02:47.844][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:47.844][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:47.846][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.858][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:47.860][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:47.862][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:02:47.863][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-06-29 16:02:47.864][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:02:47.865][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-06-29 16:02:47.867][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.874][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.884][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.891][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.901][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.907][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:47.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:47.917][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:47.919][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.925][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.933][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.933][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.934][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.935][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.935][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.936][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.937][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.938][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.938][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.939][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.940][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.940][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.941][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.942][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.943][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.943][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.944][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.945][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.945][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.946][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.956][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-06-29 16:02:47.957][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:47.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:47.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:47.963][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:47.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:47.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.971][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.971][private$selectFields] biodb.TRACE[2024-06-29 16:02:47.972][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:47.973][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:47.974][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.974][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.975][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.976][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.976][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.977][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.978][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.979][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.980][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.980][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.981][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:47.982][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.983][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.983][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.984][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.985][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:47.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:47.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:47.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:47.995][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [64199]. biodb.DEBUG[2024-06-29 16:02:47.996][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:47.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:47.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:48.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:48.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:48.003][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:48.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:48.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.010][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:48.011][private$selectFields] biodb.TRACE[2024-06-29 16:02:48.012][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:48.012][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:48.013][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:48.014][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.015][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.015][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.016][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.017][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.017][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.018][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.019][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.020][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:48.020][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:48.021][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.022][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.022][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.023][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.024][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:48.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:48.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.033][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65648]. biodb.DEBUG[2024-06-29 16:02:48.034][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:48.035][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-06-29 16:02:48.051][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:02:48.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:02:48.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.054][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:02:48.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:02:48.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.057][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:02:48.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:02:48.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.062][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:48.063][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:48.064][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.064][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.065][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:48.066][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:48.066][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.067][ef$get] fields variable is a list. biodb.INFO [2024-06-29 16:02:48.068][biodb::testThat] biodb.INFO [2024-06-29 16:02:48.069][biodb::testThat] Running test function test.annotateMzValues_real_values (" annotateMzValues() works correctly with real values. "). biodb.INFO [2024-06-29 16:02:48.070][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:02:48.071][biodb::testThat] biodb.TRACE[2024-06-29 16:02:48.073][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:48.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:48.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.076][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:48.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:48.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.079][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:02:48.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:02:48.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:48.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:48.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:48.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:48.122][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:48.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:48.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:48.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:48.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:48.129][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:48.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:48.132][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.5*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:48.134][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:48.134][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:48.136][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.5%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:48.476][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.5%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:49.077][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:49.079][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ebf8c17fa19fb0caf99d83ca8441a2ac.content" biodb.TRACE[2024-06-29 16:02:49.082][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ebf8c17fa19fb0caf99d83ca8441a2ac.request" biodb.DEBUG[2024-06-29 16:02:49.086][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:49.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:49.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:49.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:49.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:49.093][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:49.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:49.094][private$loadEntries] Creating entries from ids [1]: "3014". biodb.DEBUG[2024-06-29 16:02:49.095][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:49.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "3014". biodb.TRACE[2024-06-29 16:02:49.097][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:49.098][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:49.099][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:49.099][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:49.100][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:49.101][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:49.103][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:49.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:49.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:49.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:49.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:49.109][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:49.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:49.111][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3014". biodb.DEBUG[2024-06-29 16:02:49.112][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:49.113][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:49.114][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3014". biodb.TRACE[2024-06-29 16:02:49.454][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3014). biodb.DEBUG[2024-06-29 16:02:49.787][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:49.789][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/48c0bb0df5de824dbe83babbff8d81fe.content" biodb.TRACE[2024-06-29 16:02:49.791][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/48c0bb0df5de824dbe83babbff8d81fe.request" biodb.TRACE[2024-06-29 16:02:49.793][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3014.xml" biodb.DEBUG[2024-06-29 16:02:49.794][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:49.795][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:49.796][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:49.797][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:49.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:49.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:49.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:49.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:49.804][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:49.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:49.807][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:49.807][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:49.808][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.809][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:49.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:49.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.813][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:49.814][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:49.814][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.815][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.816][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:49.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:49.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.819][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:49.820][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:49.821][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.821][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:49.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:49.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.825][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:49.826][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:49.827][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.827][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:49.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:49.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.831][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:49.832][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:49.833][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.834][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:49.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:49.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.838][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:49.838][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:49.839][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.840][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.841][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:49.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:49.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.844][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:49.844][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:49.845][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.846][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.847][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:49.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:49.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.850][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:49.850][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:49.851][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.852][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:49.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:49.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.856][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:49.856][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:49.857][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.858][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.859][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:49.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:49.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.862][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:49.863][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:49.864][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.864][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.865][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:49.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:49.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.868][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:49.869][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:49.870][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.871][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.872][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:49.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:49.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:49.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:49.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:49.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:49.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:49.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:49.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:49.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:49.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:49.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:49.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:49.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:49.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:49.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:49.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:49.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:49.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:49.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:49.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:49.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:49.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:49.904][self$createEntryFromContent] Accession numbers: 3014. biodb.TRACE[2024-06-29 16:02:49.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:49.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:49.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:49.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:49.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:49.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:49.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:49.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:49.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:49.914][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:49.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:49.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:49.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:49.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:49.921][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:49.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:49.922][private$loadEntries] Creating entries from ids [1]: "7567". biodb.DEBUG[2024-06-29 16:02:49.923][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:49.924][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7567". biodb.TRACE[2024-06-29 16:02:49.925][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:49.926][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:49.927][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:49.928][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:49.928][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:49.929][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:49.931][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:49.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:49.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:49.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:49.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:49.938][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:49.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:49.940][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7567". biodb.DEBUG[2024-06-29 16:02:49.942][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:49.943][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:49.944][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7567". biodb.TRACE[2024-06-29 16:02:50.287][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7567). biodb.DEBUG[2024-06-29 16:02:50.622][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:50.624][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d5365299c16307afdd0b9fe7b73b123c.content" biodb.TRACE[2024-06-29 16:02:50.627][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d5365299c16307afdd0b9fe7b73b123c.request" biodb.TRACE[2024-06-29 16:02:50.629][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7567.xml" biodb.DEBUG[2024-06-29 16:02:50.630][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:50.631][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:50.632][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:50.633][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:50.634][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:50.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:50.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:50.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:50.640][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:50.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:50.643][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:50.644][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:50.645][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.645][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:50.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:50.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.649][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:50.677][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:50.678][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.678][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.680][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:50.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:50.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.683][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:50.683][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:50.684][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.685][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.686][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:50.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:50.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.689][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:50.689][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:50.690][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.691][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:50.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:50.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.694][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:50.695][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:50.696][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.696][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:50.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:50.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.700][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:50.701][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:50.702][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.702][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.703][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:50.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:50.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.706][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:50.707][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:50.707][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.708][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.709][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:50.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:50.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.712][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:50.712][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:50.713][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.714][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:50.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:50.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.718][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:50.718][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:50.719][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.720][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:50.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:50.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.724][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:50.724][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:50.725][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.726][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.726][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:50.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:50.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.729][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:50.730][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:50.731][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.731][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.732][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:50.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:50.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:50.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:50.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:50.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:50.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:50.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:50.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:50.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:50.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:50.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:50.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:50.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:50.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:50.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:50.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:50.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:50.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:50.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:50.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:50.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:50.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:50.764][self$createEntryFromContent] Accession numbers: 7567. biodb.TRACE[2024-06-29 16:02:50.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:50.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:50.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:50.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:50.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:50.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:50.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:50.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:50.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:50.774][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:50.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:50.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:50.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:50.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:50.781][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:50.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:50.783][private$loadEntries] Creating entries from ids [1]: "8021". biodb.DEBUG[2024-06-29 16:02:50.784][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:50.785][cch$loadFileContent] Trying to load 1 files from cache: [1]: "8021". biodb.TRACE[2024-06-29 16:02:50.786][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:50.786][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:50.787][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:50.788][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:50.789][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:50.789][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:50.791][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:50.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:50.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:50.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:50.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:50.798][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:50.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:50.800][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=8021". biodb.DEBUG[2024-06-29 16:02:50.802][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:50.803][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:50.804][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=8021". biodb.TRACE[2024-06-29 16:02:51.146][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=8021). biodb.DEBUG[2024-06-29 16:02:51.484][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:51.485][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6017fc384c334739eec9b216fa851a5.content" biodb.TRACE[2024-06-29 16:02:51.488][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6017fc384c334739eec9b216fa851a5.request" biodb.TRACE[2024-06-29 16:02:51.490][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8021.xml" biodb.DEBUG[2024-06-29 16:02:51.492][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:51.493][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:51.494][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:51.495][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:51.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:51.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:51.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:51.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:51.503][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:51.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:51.506][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:51.507][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:51.508][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.509][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:51.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:51.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.513][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:51.514][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:51.515][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.516][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.517][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:51.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:51.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.521][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:51.522][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:51.522][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.523][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.524][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:51.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:51.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.527][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:51.528][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:51.529][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.529][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:51.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:51.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.534][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:51.534][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:51.535][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.536][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:51.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:51.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.540][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:51.540][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:51.541][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.542][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.543][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:51.544][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:51.545][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.546][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.546][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:51.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:51.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.550][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:51.551][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:51.552][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.553][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:51.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:51.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.557][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:51.558][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:51.559][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.559][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.560][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:51.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:51.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.564][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:51.565][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:51.566][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.566][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.567][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:51.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:51.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.571][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:51.572][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:51.573][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.573][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.574][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:51.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:51.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:51.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:51.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:51.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:51.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:51.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:51.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:51.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:51.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:51.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:51.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:51.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:51.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:51.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:51.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:51.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:51.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:51.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:51.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:51.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:51.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:51.611][self$createEntryFromContent] Accession numbers: 8021. biodb.TRACE[2024-06-29 16:02:51.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:51.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:51.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:51.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:51.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:51.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:51.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:51.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:51.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:51.629][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:51.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:51.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:51.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:51.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:51.636][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:51.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:51.638][private$loadEntries] Creating entries from ids [1]: "30382". biodb.DEBUG[2024-06-29 16:02:51.639][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:51.640][cch$loadFileContent] Trying to load 1 files from cache: [1]: "30382". biodb.TRACE[2024-06-29 16:02:51.641][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:51.642][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:51.643][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:51.643][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:51.644][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:51.645][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:51.647][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:51.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:51.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:51.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:51.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:51.654][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:51.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:51.656][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30382". biodb.DEBUG[2024-06-29 16:02:51.658][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:51.658][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:51.659][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30382". biodb.TRACE[2024-06-29 16:02:52.002][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30382). biodb.DEBUG[2024-06-29 16:02:52.335][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:52.337][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/762ae1b4688e0a5ef1a1419b25f545f9.content" biodb.TRACE[2024-06-29 16:02:52.339][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/762ae1b4688e0a5ef1a1419b25f545f9.request" biodb.TRACE[2024-06-29 16:02:52.341][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/30382.xml" biodb.DEBUG[2024-06-29 16:02:52.342][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:52.343][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:52.344][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:52.345][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:52.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:52.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:52.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:52.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:52.352][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:52.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:52.354][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:52.355][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:52.356][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.356][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:52.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:52.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.360][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:52.361][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:52.361][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.362][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.363][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:52.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:52.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.366][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:52.367][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:52.367][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.368][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.369][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:52.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:52.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.372][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:52.372][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:52.373][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.374][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:52.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:52.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.378][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:52.379][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:52.379][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.380][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:52.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:52.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.384][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:52.385][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:52.386][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.387][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.388][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:52.388][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:52.389][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.390][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.391][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:52.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:52.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.394][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:52.395][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:52.395][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.396][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:52.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:52.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.400][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:52.401][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:52.401][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.402][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:52.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:52.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.406][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:52.407][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:52.408][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.408][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.409][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:52.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:52.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.412][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:52.413][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:52.414][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.414][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.415][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:52.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:52.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:52.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:52.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:52.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:52.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:52.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:52.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:52.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:52.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:52.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:52.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:52.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:52.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:52.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:52.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:52.449][self$createEntryFromContent] Accession numbers: 30382. biodb.TRACE[2024-06-29 16:02:52.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:52.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:52.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:52.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:52.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:52.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:52.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:52.459][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:52.460][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:52.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:52.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:52.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:52.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:52.467][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:52.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:52.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.475][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.475][private$selectFields] biodb.TRACE[2024-06-29 16:02:52.476][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:52.477][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:52.478][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.478][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.479][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.480][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.480][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.481][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.482][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.483][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.483][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.484][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.485][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.486][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.486][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.487][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.488][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.489][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:52.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.499][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-06-29 16:02:52.500][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:52.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:52.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:52.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:52.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:52.507][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:52.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:52.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.515][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.516][private$selectFields] biodb.TRACE[2024-06-29 16:02:52.517][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:52.517][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:52.518][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.519][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.519][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.520][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.521][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.522][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.522][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.523][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.524][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.525][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.526][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.526][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.527][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.528][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.529][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.529][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:52.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.540][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [8021]. biodb.DEBUG[2024-06-29 16:02:52.541][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:52.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:52.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:52.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:52.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:52.548][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:52.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:52.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.556][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.556][private$selectFields] biodb.TRACE[2024-06-29 16:02:52.557][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:52.565][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:52.566][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.567][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.567][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.568][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.569][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.570][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.571][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.571][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.572][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.573][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.574][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:52.574][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.575][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.576][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.576][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.577][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:52.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:52.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:52.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:52.587][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [30382]. biodb.DEBUG[2024-06-29 16:02:52.588][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:52.589][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:52.590][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:52.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:52.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:52.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:52.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:52.597][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:52.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:52.600][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.4*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:52.602][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:52.603][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:52.604][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.4%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:52.951][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.4%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:02:53.290][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:53.292][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/152225e020c3e5947a0f5a90f021cee7.content" biodb.TRACE[2024-06-29 16:02:53.295][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/152225e020c3e5947a0f5a90f021cee7.request" biodb.DEBUG[2024-06-29 16:02:53.298][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:53.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:53.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:53.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:53.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:53.304][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:53.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:53.306][private$loadEntries] Creating entries from ids [1]: "9710". biodb.DEBUG[2024-06-29 16:02:53.306][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:53.308][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9710". biodb.TRACE[2024-06-29 16:02:53.308][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:53.309][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:53.310][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:53.311][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:53.311][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:53.312][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:53.314][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:53.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:53.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:53.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:53.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:53.321][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:53.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:53.322][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9710". biodb.DEBUG[2024-06-29 16:02:53.324][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:53.325][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:53.326][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9710". biodb.TRACE[2024-06-29 16:02:53.665][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9710). biodb.DEBUG[2024-06-29 16:02:54.001][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:54.003][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b7c920ea46a15bb7175f778579142c91.content" biodb.TRACE[2024-06-29 16:02:54.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b7c920ea46a15bb7175f778579142c91.request" biodb.TRACE[2024-06-29 16:02:54.008][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9710.xml" biodb.DEBUG[2024-06-29 16:02:54.009][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:54.010][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:54.011][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:54.012][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:54.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:54.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:54.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:54.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:54.019][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:54.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:54.021][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.022][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.023][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.024][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.028][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:54.029][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:54.030][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.030][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.031][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:54.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:54.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.034][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:54.035][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:54.036][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.037][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.038][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:54.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:54.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.041][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:54.041][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:54.042][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.043][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:54.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:54.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.047][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:54.048][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:54.048][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.049][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:54.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:54.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.053][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:54.054][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:54.055][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.055][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.056][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:54.057][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.058][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.058][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.059][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:54.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.062][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:54.063][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:54.064][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.065][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:54.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:54.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.069][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:54.069][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:54.070][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.071][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.072][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:54.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:54.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.074][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:54.075][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:54.076][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.077][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.078][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:54.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:54.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.081][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:54.082][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:54.082][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.083][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.084][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:54.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:54.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:54.116][self$createEntryFromContent] Accession numbers: 9710. biodb.TRACE[2024-06-29 16:02:54.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:54.126][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:54.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:54.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:54.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:54.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:54.133][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:54.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:54.135][private$loadEntries] Creating entries from ids [1]: "65530". biodb.DEBUG[2024-06-29 16:02:54.135][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:54.137][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65530". biodb.TRACE[2024-06-29 16:02:54.138][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:54.138][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:54.139][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:54.140][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:54.141][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:54.142][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:54.144][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:54.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:54.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:54.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:54.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:54.150][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:54.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:54.152][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65530". biodb.DEBUG[2024-06-29 16:02:54.154][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:54.155][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:54.156][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65530". biodb.TRACE[2024-06-29 16:02:54.502][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65530). biodb.DEBUG[2024-06-29 16:02:54.837][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:54.838][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/bb7ff6c0bdfa280406af23f96ee06f80.content" biodb.TRACE[2024-06-29 16:02:54.841][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/bb7ff6c0bdfa280406af23f96ee06f80.request" biodb.TRACE[2024-06-29 16:02:54.843][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65530.xml" biodb.DEBUG[2024-06-29 16:02:54.844][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:54.845][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:54.846][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:54.847][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:54.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:54.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:54.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:54.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:54.854][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:54.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:54.856][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.857][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.858][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.859][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.874][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:54.875][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:54.876][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.877][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.878][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:54.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:54.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.880][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:54.881][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:54.882][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.882][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.883][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:54.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:54.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.886][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:54.887][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:54.888][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.888][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:54.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:54.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.893][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:54.893][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:54.894][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.895][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:54.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:54.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.899][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:54.900][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:54.901][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.901][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.902][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:54.903][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.904][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.904][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.905][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:54.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.908][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:54.909][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:54.910][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.910][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:54.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:54.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.915][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:54.915][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:54.916][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.917][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:54.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:54.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.921][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:54.921][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:54.922][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.923][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.924][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:54.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:54.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.927][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:54.927][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:54.928][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.929][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.930][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:54.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:54.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:54.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:54.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:54.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:54.962][self$createEntryFromContent] Accession numbers: 65530. biodb.TRACE[2024-06-29 16:02:54.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:54.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:54.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:54.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:54.972][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:54.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:54.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:54.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:54.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:54.980][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:54.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:54.981][private$loadEntries] Creating entries from ids [1]: "72338". biodb.DEBUG[2024-06-29 16:02:54.982][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:54.983][cch$loadFileContent] Trying to load 1 files from cache: [1]: "72338". biodb.TRACE[2024-06-29 16:02:54.984][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:54.985][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:54.986][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:54.987][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:54.987][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:54.988][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:54.990][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:54.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:54.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:54.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:54.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:54.997][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:54.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:54.999][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=72338". biodb.DEBUG[2024-06-29 16:02:55.001][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:55.002][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:55.003][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=72338". biodb.TRACE[2024-06-29 16:02:55.349][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=72338). biodb.DEBUG[2024-06-29 16:02:55.689][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:55.691][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e64dda61e0a44a21c5b0eb3609a4a7b.content" biodb.TRACE[2024-06-29 16:02:55.693][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e64dda61e0a44a21c5b0eb3609a4a7b.request" biodb.TRACE[2024-06-29 16:02:55.695][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/72338.xml" biodb.DEBUG[2024-06-29 16:02:55.697][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:55.697][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:55.699][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:55.700][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:55.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:55.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:55.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:55.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:55.707][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:55.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:55.710][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:55.711][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:55.711][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.712][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:55.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:55.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.716][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:55.717][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:55.717][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.718][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.719][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:55.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:55.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.722][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:55.723][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:55.724][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.725][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.726][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:55.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:55.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.728][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:55.729][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:55.730][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.731][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:55.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:55.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.735][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:55.735][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:55.736][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.737][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:55.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:55.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.741][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:55.741][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:55.742][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.743][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.744][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:55.744][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:55.745][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.746][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.747][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:55.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:55.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.750][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:55.751][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:55.751][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.752][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:55.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:55.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.756][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:55.757][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:55.757][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.758][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:55.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:55.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.762][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:55.763][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:55.764][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.764][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.765][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:55.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:55.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.768][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:55.769][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:55.770][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.770][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.771][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:55.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:55.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:55.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:55.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:55.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:55.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:55.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:55.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:55.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:55.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:55.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:55.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:55.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:55.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:55.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:55.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:55.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:55.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:55.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:55.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:55.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:55.804][self$createEntryFromContent] Accession numbers: 72338. biodb.TRACE[2024-06-29 16:02:55.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:55.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:55.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:55.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:55.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:55.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:55.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:55.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:55.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:55.821][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:55.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:55.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:55.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:55.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:55.828][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:55.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:55.830][private$loadEntries] Creating entries from ids [1]: "77926". biodb.DEBUG[2024-06-29 16:02:55.831][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:55.832][cch$loadFileContent] Trying to load 1 files from cache: [1]: "77926". biodb.TRACE[2024-06-29 16:02:55.833][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:55.834][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:55.834][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:55.835][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:55.836][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:55.837][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:55.839][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:55.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:55.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:55.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:55.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:55.845][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:55.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:55.847][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77926". biodb.DEBUG[2024-06-29 16:02:55.849][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:55.850][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:55.851][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77926". biodb.TRACE[2024-06-29 16:02:56.301][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77926). biodb.DEBUG[2024-06-29 16:02:56.636][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:56.637][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9ad4fcb4fcba98dcbec5ee6292352f7b.content" biodb.TRACE[2024-06-29 16:02:56.640][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9ad4fcb4fcba98dcbec5ee6292352f7b.request" biodb.TRACE[2024-06-29 16:02:56.642][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/77926.xml" biodb.DEBUG[2024-06-29 16:02:56.643][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:56.644][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:56.645][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:56.647][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:56.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:56.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:56.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:56.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:56.654][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:56.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:56.656][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:56.657][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:56.658][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.658][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:56.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:56.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.663][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:56.664][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:56.664][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.665][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.666][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:56.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:56.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.669][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:56.670][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:56.671][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.672][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.673][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:56.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:56.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.676][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:56.677][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:56.678][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.678][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:56.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:56.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.682][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:56.683][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:56.684][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.685][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.686][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:56.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:56.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.689][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:56.689][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:56.690][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.691][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.692][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:56.693][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:56.693][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.694][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.695][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:56.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:56.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.698][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:56.699][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:56.700][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.700][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:56.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:56.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.705][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:56.705][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:56.706][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.707][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:56.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:56.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.711][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:56.712][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:56.713][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.713][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.714][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:56.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:56.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.717][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:56.718][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:56.719][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.720][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.721][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:56.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:56.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:56.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:56.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:56.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:56.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:56.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:56.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:56.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:56.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:56.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:56.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:56.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:56.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:56.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:56.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:56.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:56.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:56.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:56.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:56.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:56.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.758][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:56.759][self$createEntryFromContent] Accession numbers: 77926. biodb.TRACE[2024-06-29 16:02:56.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:56.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:56.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:56.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:56.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:56.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:56.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:56.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:56.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:56.769][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:56.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:56.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:56.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:56.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:56.776][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:56.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:56.778][private$loadEntries] Creating entries from ids [1]: "82369". biodb.DEBUG[2024-06-29 16:02:56.779][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:56.780][cch$loadFileContent] Trying to load 1 files from cache: [1]: "82369". biodb.TRACE[2024-06-29 16:02:56.781][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:56.782][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:56.783][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:56.784][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:56.784][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:56.785][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:56.787][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:56.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:56.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:56.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:56.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:56.795][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:56.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:56.796][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=82369". biodb.DEBUG[2024-06-29 16:02:56.798][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:56.799][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:56.800][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=82369". biodb.TRACE[2024-06-29 16:02:57.146][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=82369). biodb.DEBUG[2024-06-29 16:02:57.481][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:57.483][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/141011223a89b45316c20d1fd91b47fd.content" biodb.TRACE[2024-06-29 16:02:57.486][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/141011223a89b45316c20d1fd91b47fd.request" biodb.TRACE[2024-06-29 16:02:57.488][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/82369.xml" biodb.DEBUG[2024-06-29 16:02:57.489][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:57.490][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:57.491][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:57.492][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:57.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:57.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:57.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:57.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:57.499][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:57.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:57.501][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:57.502][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:57.503][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.504][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:57.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:57.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.508][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:57.509][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:57.509][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.510][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.511][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:57.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:57.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.514][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:57.515][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:57.515][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.516][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.517][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:57.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:57.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.520][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:57.521][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:57.522][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.522][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:57.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:57.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.526][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:57.527][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:57.528][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.528][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:57.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:57.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.533][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:57.534][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:57.534][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.535][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.536][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:57.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:57.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.539][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:57.540][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:57.541][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.541][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.542][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:57.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:57.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.545][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:57.551][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:57.557][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.557][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:57.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:57.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.562][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:57.562][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:57.563][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.564][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:57.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:57.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.568][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:57.569][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:57.569][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.570][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.571][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:57.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:57.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.574][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:57.574][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:57.575][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.576][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.577][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:57.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:57.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:57.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:57.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:57.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:57.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:57.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:57.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:57.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:57.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:57.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:57.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:57.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:57.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:57.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:57.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:57.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:57.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:57.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:57.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:57.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:57.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:57.609][self$createEntryFromContent] Accession numbers: 82369. biodb.TRACE[2024-06-29 16:02:57.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:57.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:57.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:57.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:57.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:57.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:57.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:57.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:57.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:57.618][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:57.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:57.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:57.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:57.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:57.625][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:57.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:57.627][private$loadEntries] Creating entries from ids [1]: "90204". biodb.DEBUG[2024-06-29 16:02:57.628][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:57.629][cch$loadFileContent] Trying to load 1 files from cache: [1]: "90204". biodb.TRACE[2024-06-29 16:02:57.630][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:57.630][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:57.631][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:57.632][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:57.633][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:57.633][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:57.635][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:57.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:57.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:57.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:57.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:57.642][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:57.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:57.644][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=90204". biodb.DEBUG[2024-06-29 16:02:57.646][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:57.647][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:57.648][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=90204". biodb.TRACE[2024-06-29 16:02:57.997][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=90204). biodb.DEBUG[2024-06-29 16:02:58.335][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:58.336][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/bd50d349ae7e6e2bbccffc7e4e5f18de.content" biodb.TRACE[2024-06-29 16:02:58.339][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/bd50d349ae7e6e2bbccffc7e4e5f18de.request" biodb.TRACE[2024-06-29 16:02:58.341][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/90204.xml" biodb.DEBUG[2024-06-29 16:02:58.342][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:58.343][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:58.344][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:58.345][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:58.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:58.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:58.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:58.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:58.352][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:58.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:58.354][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:58.355][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:58.356][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.356][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:58.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:58.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.360][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:58.361][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:58.362][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.362][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.363][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:58.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:58.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.366][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:58.367][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:58.368][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.368][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.369][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:58.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:58.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.372][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:58.373][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:58.374][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.375][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.376][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:58.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:58.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.379][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:58.380][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:58.380][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.381][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:58.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:58.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.385][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:58.386][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:58.386][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.387][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.388][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:58.389][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:58.389][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.390][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.391][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:58.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:58.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.394][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:58.394][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:58.395][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.396][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:58.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:58.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.400][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:58.400][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:58.401][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.402][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:58.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:58.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.406][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:58.406][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:58.407][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.408][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.408][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:58.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:58.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.411][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:58.412][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:58.413][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.414][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.415][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:58.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:58.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:58.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:58.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:58.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:58.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:58.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:58.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:58.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:58.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:58.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:58.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:58.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:58.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:58.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:58.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:58.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:58.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:58.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:58.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:58.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:58.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:58.447][self$createEntryFromContent] Accession numbers: 90204. biodb.TRACE[2024-06-29 16:02:58.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:58.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:58.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:58.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:58.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:58.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:58.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:58.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:58.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:58.456][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:58.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:58.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:58.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:58.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:58.463][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:58.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:58.465][private$loadEntries] Creating entries from ids [1]: "132793". biodb.DEBUG[2024-06-29 16:02:58.465][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:02:58.467][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132793". biodb.TRACE[2024-06-29 16:02:58.468][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:02:58.468][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:02:58.469][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:02:58.470][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:02:58.471][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:02:58.471][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:02:58.474][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:58.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:58.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:58.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:58.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:58.480][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:58.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:58.482][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132793". biodb.DEBUG[2024-06-29 16:02:58.484][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:58.485][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:58.486][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132793". biodb.TRACE[2024-06-29 16:02:58.834][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132793). biodb.DEBUG[2024-06-29 16:02:59.169][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:02:59.171][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a797bec3bbec3ca7a5b4b96140b735a3.content" biodb.TRACE[2024-06-29 16:02:59.184][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a797bec3bbec3ca7a5b4b96140b735a3.request" biodb.TRACE[2024-06-29 16:02:59.186][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132793.xml" biodb.DEBUG[2024-06-29 16:02:59.187][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:02:59.188][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:02:59.189][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:02:59.190][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:59.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:59.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:59.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:59.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:59.197][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:59.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:59.199][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:59.199][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:59.200][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.201][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:59.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:59.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.205][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:59.205][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:59.206][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.207][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.208][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:02:59.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:02:59.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.211][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:59.211][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:59.212][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.213][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.213][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:02:59.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:02:59.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.216][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:59.217][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:59.218][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.218][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:02:59.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:02:59.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.222][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:59.223][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:59.224][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.224][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.225][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:02:59.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:02:59.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.228][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:59.229][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:59.230][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.230][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.231][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:59.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:02:59.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.234][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:59.235][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:59.235][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.236][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.237][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:02:59.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:59.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.240][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:59.241][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:59.241][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.242][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:59.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:02:59.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.246][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:59.246][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:59.247][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.248][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.249][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:02:59.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:02:59.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.252][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:59.252][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:59.253][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.254][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.255][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:02:59.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:02:59.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.258][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:59.258][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:59.259][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.260][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.261][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:02:59.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:02:59.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:59.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:59.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:59.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:59.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:59.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:59.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:59.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:59.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:59.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:59.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:59.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:59.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:02:59.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:02:59.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:59.293][self$createEntryFromContent] Accession numbers: 132793. biodb.TRACE[2024-06-29 16:02:59.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:59.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:59.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:59.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:59.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:02:59.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:02:59.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:02:59.302][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:02:59.304][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:59.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:59.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:59.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:59.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:59.311][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:59.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:59.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.319][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.319][private$selectFields] biodb.TRACE[2024-06-29 16:02:59.320][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:59.321][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:59.321][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.322][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.323][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.324][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.324][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.325][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.326][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.326][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.327][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.328][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.328][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.329][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.330][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.331][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.332][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.332][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:59.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.342][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65530]. biodb.DEBUG[2024-06-29 16:02:59.343][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:59.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:59.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:59.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:59.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:59.350][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:59.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:59.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.357][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.358][private$selectFields] biodb.TRACE[2024-06-29 16:02:59.359][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:59.359][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:59.360][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.361][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.361][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.362][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.363][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.364][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.364][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.365][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.366][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.366][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.367][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.368][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.369][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.369][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.370][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.371][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:59.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.381][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [90204]. biodb.DEBUG[2024-06-29 16:02:59.381][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:59.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:59.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:59.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:59.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:59.388][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:59.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:02:59.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.396][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.396][private$selectFields] biodb.TRACE[2024-06-29 16:02:59.397][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:02:59.398][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:02:59.398][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.399][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.400][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.400][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.401][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.402][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.403][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.403][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.404][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.405][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.406][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:02:59.406][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.407][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.408][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.408][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.409][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:02:59.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:02:59.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:02:59.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:02:59.419][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [132793]. biodb.DEBUG[2024-06-29 16:02:59.419][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:02:59.420][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:02:59.422][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:02:59.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:02:59.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:02:59.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:02:59.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:02:59.428][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:02:59.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:02:59.436][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:02:59.439][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:02:59.439][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:02:59.441][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:02:59.774][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:03:00.108][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:00.109][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9686ce9c957a368dd8f5b4cc9c5b15b3.content" biodb.TRACE[2024-06-29 16:03:00.112][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9686ce9c957a368dd8f5b4cc9c5b15b3.request" biodb.DEBUG[2024-06-29 16:03:00.114][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:00.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:00.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:00.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:00.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:00.121][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:00.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:00.122][private$loadEntries] Creating entries from ids [1]: "131378". biodb.DEBUG[2024-06-29 16:03:00.123][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:00.124][cch$loadFileContent] Trying to load 1 files from cache: [1]: "131378". biodb.TRACE[2024-06-29 16:03:00.125][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:00.126][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:00.127][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:00.127][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:00.128][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:00.129][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:00.131][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:00.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:00.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:00.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:00.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:00.137][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:00.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:00.139][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=131378". biodb.DEBUG[2024-06-29 16:03:00.140][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:00.141][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:00.142][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=131378". biodb.TRACE[2024-06-29 16:03:00.480][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=131378). biodb.DEBUG[2024-06-29 16:03:00.815][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:00.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5b759b1dd2dc96585e60782e41aa0772.content" biodb.TRACE[2024-06-29 16:03:00.820][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5b759b1dd2dc96585e60782e41aa0772.request" biodb.TRACE[2024-06-29 16:03:00.821][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/131378.xml" biodb.DEBUG[2024-06-29 16:03:00.823][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:00.824][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:00.824][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:00.826][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:00.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:00.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:00.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:00.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:00.833][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:00.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:00.835][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:00.836][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:00.836][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.837][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:00.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:00.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.841][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:00.842][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:00.842][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.843][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.844][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:00.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:00.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.847][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:00.848][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:00.848][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.849][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:00.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:00.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.853][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:00.854][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:00.854][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.855][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:00.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:00.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.859][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:00.860][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:00.860][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.861][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:00.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:00.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.865][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:00.866][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:00.867][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.867][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.868][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:00.869][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:00.870][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.870][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.871][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:00.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:00.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.874][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:00.875][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:00.876][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.876][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:00.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:00.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.880][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:00.881][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:00.882][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.882][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:00.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:00.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.886][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:00.887][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:00.888][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.888][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.889][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:00.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:00.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.892][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:00.893][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:00.894][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.894][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.895][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:00.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:00.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:00.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:00.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:00.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:00.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:00.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:00.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:00.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:00.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:00.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:00.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:00.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:00.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:00.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:00.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:00.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:00.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:00.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:00.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:00.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:00.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:00.928][self$createEntryFromContent] Accession numbers: 131378. biodb.TRACE[2024-06-29 16:03:00.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:00.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:00.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:00.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:00.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:00.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:00.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:00.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:00.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:00.937][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:00.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:00.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:00.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:00.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:00.944][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:00.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:00.945][private$loadEntries] Creating entries from ids [1]: "214202". biodb.DEBUG[2024-06-29 16:03:00.946][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:00.947][cch$loadFileContent] Trying to load 1 files from cache: [1]: "214202". biodb.TRACE[2024-06-29 16:03:00.948][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:00.949][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:00.950][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:00.951][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:00.952][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:00.952][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:00.954][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:00.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:00.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:00.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:00.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:00.961][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:00.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:00.962][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=214202". biodb.DEBUG[2024-06-29 16:03:00.964][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:00.965][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:00.966][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=214202". biodb.TRACE[2024-06-29 16:03:01.310][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=214202). biodb.DEBUG[2024-06-29 16:03:01.644][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:01.646][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf9a3fb7c59af59e06fd510ceb170574.content" biodb.TRACE[2024-06-29 16:03:01.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf9a3fb7c59af59e06fd510ceb170574.request" biodb.TRACE[2024-06-29 16:03:01.650][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/214202.xml" biodb.DEBUG[2024-06-29 16:03:01.651][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:01.652][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:01.653][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:01.654][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:01.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:01.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:01.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:01.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:01.661][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:01.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:01.663][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:01.664][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:01.665][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.666][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:01.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:01.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.670][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:01.670][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:01.671][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.672][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.673][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:01.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:01.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.676][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:01.677][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:01.677][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.678][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.679][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:01.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:01.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.682][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:01.683][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:01.684][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.684][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:01.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:01.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.689][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:01.689][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:01.690][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.691][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:01.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:01.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.694][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:01.695][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:01.696][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.697][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.709][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:01.710][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:01.711][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.711][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.712][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:01.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:01.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.715][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:01.716][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:01.716][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.717][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:01.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:01.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.721][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:01.722][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:01.723][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.723][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:01.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:01.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.728][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:01.728][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:01.729][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.730][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.730][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:01.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:01.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.733][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:01.734][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:01.735][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.735][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.736][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:01.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:01.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:01.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:01.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:01.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:01.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:01.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:01.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:01.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:01.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:01.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:01.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:01.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:01.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:01.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:01.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.758][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:01.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:01.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:01.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:01.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:01.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:01.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:01.768][self$createEntryFromContent] Accession numbers: 214202. biodb.TRACE[2024-06-29 16:03:01.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:01.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:01.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:01.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:01.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:01.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:01.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:01.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:01.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:01.778][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.2*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:01.780][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:01.781][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:01.782][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.2%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:03:02.154][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.2%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:03:02.489][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:02.491][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5d833e77a1be58060d0c3916a1e1b293.content" biodb.TRACE[2024-06-29 16:03:02.494][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5d833e77a1be58060d0c3916a1e1b293.request" biodb.DEBUG[2024-06-29 16:03:02.496][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:02.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:02.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:02.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:02.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:02.503][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:02.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:02.505][private$loadEntries] Creating entries from ids [1]: "51836". biodb.DEBUG[2024-06-29 16:03:02.505][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:02.506][cch$loadFileContent] Trying to load 1 files from cache: [1]: "51836". biodb.TRACE[2024-06-29 16:03:02.507][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:02.508][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:02.509][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:02.510][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:02.510][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:02.511][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:02.513][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:02.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:02.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:02.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:02.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:02.520][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:02.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:02.521][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51836". biodb.DEBUG[2024-06-29 16:03:02.523][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:02.524][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:02.525][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51836". biodb.TRACE[2024-06-29 16:03:02.869][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51836). biodb.DEBUG[2024-06-29 16:03:03.208][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:03.210][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1fe2079ad59bca4bc82b2cd14ed8e8a1.content" biodb.TRACE[2024-06-29 16:03:03.213][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1fe2079ad59bca4bc82b2cd14ed8e8a1.request" biodb.TRACE[2024-06-29 16:03:03.214][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/51836.xml" biodb.DEBUG[2024-06-29 16:03:03.216][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:03.217][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:03.218][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:03.219][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:03.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:03.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:03.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:03.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:03.226][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:03.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:03.228][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:03.229][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:03.230][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.230][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:03.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:03.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.234][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:03.235][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:03.236][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.237][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.237][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:03.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:03.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.240][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:03.241][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:03.242][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.243][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.243][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:03.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:03.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.246][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:03.247][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:03.248][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.248][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:03.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:03.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.253][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:03.253][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:03.254][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.255][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.256][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:03.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:03.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.259][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:03.259][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:03.260][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.261][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.262][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:03.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:03.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.265][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:03.265][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:03.266][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.267][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.268][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:03.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:03.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.271][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:03.271][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:03.272][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.273][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:03.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:03.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.277][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:03.277][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:03.278][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.279][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.280][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:03.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:03.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.283][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:03.284][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:03.284][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.285][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.286][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:03.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:03.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.289][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:03.290][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:03.290][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.291][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.292][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:03.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:03.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:03.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:03.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.297][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:03.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:03.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:03.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:03.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:03.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:03.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:03.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:03.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:03.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:03.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:03.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:03.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:03.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:03.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:03.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:03.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:03.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:03.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:03.421][self$createEntryFromContent] Accession numbers: 51836. biodb.TRACE[2024-06-29 16:03:03.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:03.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:03.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:03.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:03.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:03.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:03.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:03.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:03.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:03.454][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:03.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:03.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:03.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:03.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:03.461][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:03.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:03.472][private$loadEntries] Creating entries from ids [1]: "51837". biodb.DEBUG[2024-06-29 16:03:03.473][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:03.474][cch$loadFileContent] Trying to load 1 files from cache: [1]: "51837". biodb.TRACE[2024-06-29 16:03:03.475][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:03.476][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:03.477][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:03.478][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:03.478][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:03.479][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:03.481][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:03.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:03.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:03.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:03.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:03.488][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:03.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:03.489][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51837". biodb.DEBUG[2024-06-29 16:03:03.491][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:03.492][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:03.493][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51837". biodb.TRACE[2024-06-29 16:03:03.839][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51837). biodb.DEBUG[2024-06-29 16:03:04.173][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:04.175][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1588f004fb5de8667ae1af7433b2932e.content" biodb.TRACE[2024-06-29 16:03:04.177][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1588f004fb5de8667ae1af7433b2932e.request" biodb.TRACE[2024-06-29 16:03:04.179][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/51837.xml" biodb.DEBUG[2024-06-29 16:03:04.181][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:04.182][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:04.182][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:04.184][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:04.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:04.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:04.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:04.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:04.190][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:04.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:04.193][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:04.194][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:04.195][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.195][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:04.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:04.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.199][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:04.200][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:04.200][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.201][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.202][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:04.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:04.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.205][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:04.206][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:04.206][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.207][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.208][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:04.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:04.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.211][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:04.212][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:04.212][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.213][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:04.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:04.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.217][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:04.217][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:04.218][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.219][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:04.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:04.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.223][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:04.223][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:04.224][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.225][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.226][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:04.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:04.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.229][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:04.230][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:04.230][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.231][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.232][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:04.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:04.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.235][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:04.236][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:04.236][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.237][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:04.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:04.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.241][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:04.242][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:04.243][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.243][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:04.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:04.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.247][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:04.248][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:04.249][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.250][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.250][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:04.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:04.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.253][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:04.254][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:04.255][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.255][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.256][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:04.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:04.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:04.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:04.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:04.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:04.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:04.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:04.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:04.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:04.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:04.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:04.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:04.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:04.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:04.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:04.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:04.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:04.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:04.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:04.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:04.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:04.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:04.289][self$createEntryFromContent] Accession numbers: 51837. biodb.TRACE[2024-06-29 16:03:04.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:04.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:04.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:04.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:04.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:04.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:04.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:04.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:04.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:04.299][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:04.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:04.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:04.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:04.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:04.306][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:04.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:04.307][private$loadEntries] Creating entries from ids [1]: "132205". biodb.DEBUG[2024-06-29 16:03:04.308][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:04.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132205". biodb.TRACE[2024-06-29 16:03:04.310][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:04.311][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:04.312][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:04.313][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:04.313][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:04.314][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:04.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:04.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:04.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:04.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:04.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:04.323][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:04.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:04.325][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132205". biodb.DEBUG[2024-06-29 16:03:04.327][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:04.327][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:04.328][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132205". biodb.TRACE[2024-06-29 16:03:04.666][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132205). biodb.DEBUG[2024-06-29 16:03:04.998][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:05.000][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0bfa2ac1d845d7db5b781e9a39528bb3.content" biodb.TRACE[2024-06-29 16:03:05.002][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0bfa2ac1d845d7db5b781e9a39528bb3.request" biodb.TRACE[2024-06-29 16:03:05.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132205.xml" biodb.DEBUG[2024-06-29 16:03:05.006][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:05.007][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:05.008][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:05.009][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.016][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.018][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:05.019][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:05.020][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.020][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:05.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:05.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.024][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:05.025][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:05.026][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.026][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.027][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:05.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:05.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.030][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:05.031][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:05.032][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.032][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.033][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:05.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:05.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.036][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:05.037][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:05.038][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.038][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:05.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:05.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.042][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:05.043][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:05.044][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.044][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:05.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:05.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.048][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:05.049][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:05.050][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.050][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.051][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:05.052][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.053][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.053][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.054][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:05.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.057][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:05.058][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:05.059][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.059][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:05.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:05.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.063][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:05.064][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:05.065][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.065][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:05.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:05.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.078][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:05.079][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:05.080][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.081][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.082][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:05.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:05.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.085][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:05.086][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:05.086][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.087][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.088][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:05.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:05.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:05.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:05.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:05.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:05.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:05.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:05.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:05.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:05.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:05.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:05.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:05.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:05.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:05.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:05.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.121][self$createEntryFromContent] Accession numbers: 132205. biodb.TRACE[2024-06-29 16:03:05.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.130][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:05.131][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.138][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.146][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.146][private$selectFields] biodb.TRACE[2024-06-29 16:03:05.147][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:05.148][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:05.148][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.149][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.150][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.151][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.152][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.152][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.153][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.154][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.155][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.155][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.156][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.157][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.158][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.158][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.159][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.160][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:05.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.170][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [51836]. biodb.DEBUG[2024-06-29 16:03:05.171][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.178][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.185][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.186][private$selectFields] biodb.TRACE[2024-06-29 16:03:05.187][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:05.187][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:05.188][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.189][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.190][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.190][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.191][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.192][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.193][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.193][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.194][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.195][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.196][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.196][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.197][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.198][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.198][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.199][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:05.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.209][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [51837]. biodb.DEBUG[2024-06-29 16:03:05.210][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.216][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.224][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.225][private$selectFields] biodb.TRACE[2024-06-29 16:03:05.225][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:05.226][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:05.227][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.227][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.228][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.229][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.229][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.230][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.231][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.232][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.232][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.233][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.234][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.234][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.235][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.236][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.237][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.238][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:05.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.247][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [132205]. biodb.DEBUG[2024-06-29 16:03:05.248][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:05.248][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:05.266][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.272][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:05.275][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:05.277][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:05.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-06-29 16:03:05.279][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:05.280][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-06-29 16:03:05.282][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.288][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.299][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:05.302][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:05.303][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-06-29 16:03:05.304][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:05.305][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-06-29 16:03:05.306][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.313][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.323][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.330][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.346][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:05.347][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.354][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.361][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.362][private$selectFields] biodb.TRACE[2024-06-29 16:03:05.362][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:05.363][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:05.364][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.364][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.365][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.366][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.366][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.367][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.368][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.368][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.369][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.370][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.371][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.371][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.372][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.373][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.373][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.374][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:05.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.383][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2024-06-29 16:03:05.384][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.391][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.398][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.399][private$selectFields] biodb.TRACE[2024-06-29 16:03:05.400][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:05.400][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:05.401][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.402][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.402][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.403][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.404][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.405][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.405][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.406][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.407][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.407][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.408][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.409][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.410][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.410][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.411][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.412][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:05.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.421][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:03:05.422][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.429][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.436][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.437][private$selectFields] biodb.TRACE[2024-06-29 16:03:05.438][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:05.438][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:05.439][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.440][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.441][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.442][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.442][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.443][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.444][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.444][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.445][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.446][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.447][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.447][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.448][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.449][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.449][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.450][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:05.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.460][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2024-06-29 16:03:05.461][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:05.461][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:05.463][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.470][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:05.473][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:05.475][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:05.476][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-06-29 16:03:05.477][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:05.478][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-06-29 16:03:05.480][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.486][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.497][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.504][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.514][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:05.517][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:05.518][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-06-29 16:03:05.518][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:05.519][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-06-29 16:03:05.522][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.529][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.539][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.546][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.556][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.563][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.574][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:05.575][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.582][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.589][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.594][private$selectFields] biodb.TRACE[2024-06-29 16:03:05.595][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:05.596][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:05.597][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.597][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.598][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.599][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.599][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.600][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.601][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.602][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.602][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.603][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.604][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.605][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.605][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.606][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.607][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.607][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:05.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.617][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:03:05.618][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.624][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.631][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.632][private$selectFields] biodb.TRACE[2024-06-29 16:03:05.633][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:05.633][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:05.634][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.635][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.635][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.636][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.637][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.637][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.638][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.639][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.640][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.640][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.641][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.642][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.642][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.643][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.644][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.644][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:05.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.650][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.654][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-06-29 16:03:05.654][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.661][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.669][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.669][private$selectFields] biodb.TRACE[2024-06-29 16:03:05.670][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:05.671][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:05.671][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.672][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.673][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.674][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.674][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.675][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.676][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.677][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.677][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.678][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.679][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.680][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.680][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.681][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.682][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.683][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:05.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.692][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-06-29 16:03:05.693][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:05.694][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:05.695][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.702][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:05.705][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:05.707][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:05.708][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26d0872875c47c33e8205aa7124e0486". biodb.TRACE[2024-06-29 16:03:05.709][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:05.710][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content". biodb.DEBUG[2024-06-29 16:03:05.712][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.719][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.729][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.736][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.747][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.753][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.764][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.771][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.781][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.787][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.798][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.804][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.815][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.821][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.831][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.838][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.854][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:05.856][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:05.857][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-06-29 16:03:05.858][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:05.859][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-06-29 16:03:05.861][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.867][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.877][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.884][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.893][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.900][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:05.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:05.910][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:05.911][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.917][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.925][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.925][private$selectFields] biodb.TRACE[2024-06-29 16:03:05.926][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:05.927][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:05.928][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.928][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.929][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.930][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.930][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.931][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.932][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.933][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.933][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.934][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.935][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.935][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.936][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.937][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.937][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.938][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:05.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.948][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-06-29 16:03:05.949][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.956][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.963][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.964][private$selectFields] biodb.TRACE[2024-06-29 16:03:05.964][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:05.965][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:05.966][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.966][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.967][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.968][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.969][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.969][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.970][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.971][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.972][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.972][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.973][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:05.974][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.974][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.975][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.976][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.976][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:05.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.986][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-06-29 16:03:05.987][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:05.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:05.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:05.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:05.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:05.994][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:05.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:05.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:05.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:05.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:05.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:06.001][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:06.001][private$selectFields] biodb.TRACE[2024-06-29 16:03:06.002][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:06.003][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:06.003][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:06.004][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.005][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.006][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.006][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:06.007][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.008][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.008][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.009][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:06.010][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:06.011][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:06.011][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.012][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.013][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.014][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:06.014][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:06.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:06.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:06.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:06.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:06.024][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-06-29 16:03:06.025][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:06.025][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:06.042][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:06.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:06.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:06.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:06.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:06.049][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:06.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:06.051][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.7*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:06.054][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:06.055][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:06.056][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.7%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:03:06.391][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.7%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:03:06.727][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:06.729][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2b6f29bb7a7663ff23fb5e7dcae5c27f.content" biodb.TRACE[2024-06-29 16:03:06.731][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2b6f29bb7a7663ff23fb5e7dcae5c27f.request" biodb.DEBUG[2024-06-29 16:03:06.734][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:06.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:06.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:06.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:06.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:06.741][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:06.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:06.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:06.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:06.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:06.751][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:06.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:06.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:06.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:06.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:06.758][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:06.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:06.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:06.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:06.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:06.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:06.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:06.776][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:06.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:06.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:06.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:06.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:06.783][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:06.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:06.784][private$loadEntries] Creating entries from ids [1]: "28243". biodb.DEBUG[2024-06-29 16:03:06.785][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:06.786][cch$loadFileContent] Trying to load 1 files from cache: [1]: "28243". biodb.TRACE[2024-06-29 16:03:06.787][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:06.788][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:06.789][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:06.789][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:06.790][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:06.791][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:06.793][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:06.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:06.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:06.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:06.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:06.800][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:06.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:06.801][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=28243". biodb.DEBUG[2024-06-29 16:03:06.803][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:06.804][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:06.805][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=28243". biodb.TRACE[2024-06-29 16:03:07.167][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=28243). biodb.DEBUG[2024-06-29 16:03:07.508][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:07.510][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/177c3a227615d232b537605885883911.content" biodb.TRACE[2024-06-29 16:03:07.513][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/177c3a227615d232b537605885883911.request" biodb.TRACE[2024-06-29 16:03:07.515][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/28243.xml" biodb.DEBUG[2024-06-29 16:03:07.516][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:07.517][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:07.518][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:07.519][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:07.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:07.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:07.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:07.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:07.526][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:07.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:07.528][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:07.529][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:07.530][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.530][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:07.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:07.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.534][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:07.535][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:07.536][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.537][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.538][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:07.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:07.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.540][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:07.541][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:07.542][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.542][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:07.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:07.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.546][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:07.547][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:07.548][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.549][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:07.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:07.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.552][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:07.553][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:07.554][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.555][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.556][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:07.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:07.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.559][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:07.560][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:07.561][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.561][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.562][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:07.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:07.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.565][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:07.566][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.567][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.567][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.568][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:07.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.571][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:07.572][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:07.573][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.573][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:07.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:07.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.578][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:07.578][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:07.579][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.580][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:07.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:07.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.584][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:07.584][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:07.585][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.586][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.587][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:07.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:07.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.590][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:07.590][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:07.591][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.592][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.593][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:07.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:07.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:07.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:07.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:07.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:07.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:07.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:07.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:07.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:07.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:07.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:07.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:07.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:07.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:07.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:07.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:07.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:07.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:07.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:07.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:07.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:07.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:07.625][self$createEntryFromContent] Accession numbers: 28243. biodb.TRACE[2024-06-29 16:03:07.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:07.634][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:07.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:07.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:07.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:07.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:07.641][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:07.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:07.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:07.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:07.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:07.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:07.652][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:07.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:07.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:07.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:07.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:07.658][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:07.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:07.660][private$loadEntries] Creating entries from ids [1]: "70786". biodb.DEBUG[2024-06-29 16:03:07.660][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:07.662][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70786". biodb.TRACE[2024-06-29 16:03:07.662][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:07.663][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:07.664][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:07.665][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:07.666][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:07.666][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:07.668][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:07.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:07.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:07.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:07.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:07.675][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:07.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:07.677][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70786". biodb.DEBUG[2024-06-29 16:03:07.679][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:07.679][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:07.680][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70786". biodb.TRACE[2024-06-29 16:03:08.038][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70786). biodb.DEBUG[2024-06-29 16:03:08.442][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:08.443][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ea24f2a708fc4a90f6eff28b49d993c4.content" biodb.TRACE[2024-06-29 16:03:08.446][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ea24f2a708fc4a90f6eff28b49d993c4.request" biodb.TRACE[2024-06-29 16:03:08.448][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70786.xml" biodb.DEBUG[2024-06-29 16:03:08.449][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:08.450][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:08.451][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:08.452][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:08.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:08.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:08.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:08.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:08.459][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:08.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:08.461][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:08.462][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:08.463][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.463][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:08.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:08.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.467][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:08.468][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:08.469][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.470][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.470][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:08.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:08.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.473][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:08.474][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:08.475][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.475][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.476][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:08.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:08.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.479][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:08.480][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:08.481][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.481][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:08.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:08.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.485][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:08.486][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:08.487][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.497][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:08.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:08.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.501][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:08.501][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:08.502][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.503][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.504][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:08.504][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:08.505][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.506][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.506][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:08.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:08.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.509][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:08.510][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:08.511][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.511][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:08.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:08.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.515][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:08.516][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:08.516][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.517][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.518][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:08.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:08.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.521][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:08.522][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:08.522][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.523][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.524][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:08.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:08.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.527][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:08.527][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:08.528][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.529][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.529][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:08.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:08.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:08.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:08.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:08.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:08.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:08.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:08.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:08.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:08.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:08.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:08.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:08.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:08.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:08.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:08.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:08.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:08.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:08.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:08.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:08.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:08.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:08.560][self$createEntryFromContent] Accession numbers: 70786. biodb.TRACE[2024-06-29 16:03:08.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:08.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:08.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:08.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:08.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:08.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:08.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:08.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:08.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:08.570][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:08.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:08.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:08.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:08.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:08.576][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:08.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:08.578][private$loadEntries] Creating entries from ids [1]: "78144". biodb.DEBUG[2024-06-29 16:03:08.579][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:08.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78144". biodb.TRACE[2024-06-29 16:03:08.581][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:08.581][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:08.582][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:08.583][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:08.584][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:08.584][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:08.586][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:08.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:08.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:08.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:08.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:08.593][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:08.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:08.594][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78144". biodb.DEBUG[2024-06-29 16:03:08.596][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:08.597][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:08.598][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78144". biodb.TRACE[2024-06-29 16:03:08.943][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78144). biodb.DEBUG[2024-06-29 16:03:09.294][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:09.296][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ede5a640bd42c7611e16282ef185b74.content" biodb.TRACE[2024-06-29 16:03:09.298][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ede5a640bd42c7611e16282ef185b74.request" biodb.TRACE[2024-06-29 16:03:09.300][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78144.xml" biodb.DEBUG[2024-06-29 16:03:09.301][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:09.302][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:09.303][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:09.304][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:09.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:09.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:09.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:09.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:09.311][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:09.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:09.313][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:09.314][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:09.315][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.315][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:09.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:09.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.319][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:09.320][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:09.321][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.322][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.323][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:09.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:09.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.325][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:09.326][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:09.327][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.328][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:09.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:09.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.331][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:09.332][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:09.333][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.333][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.334][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:09.335][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:09.336][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.337][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.337][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:09.338][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:09.339][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.340][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.340][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:09.341][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:09.342][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.343][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.343][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:09.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:09.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.346][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:09.347][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:09.348][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.348][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:09.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:09.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.352][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:09.353][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:09.354][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.354][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.355][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:09.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:09.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.358][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:09.359][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:09.359][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.360][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.361][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:09.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:09.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.364][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:09.365][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:09.366][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.366][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.367][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:09.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:09.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:09.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:09.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:09.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:09.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:09.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:09.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:09.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:09.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:09.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:09.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:09.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:09.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:09.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:09.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:09.399][self$createEntryFromContent] Accession numbers: 78144. biodb.TRACE[2024-06-29 16:03:09.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:09.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:09.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:09.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:09.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:09.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:09.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:09.408][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:09.409][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:09.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:09.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:09.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:09.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:09.416][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:09.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:09.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.423][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.424][private$selectFields] biodb.TRACE[2024-06-29 16:03:09.425][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:09.426][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:09.426][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.427][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.428][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.428][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.429][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.434][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.438][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.439][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.439][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.440][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.441][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.442][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.442][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.443][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.444][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.444][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:09.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.454][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:03:09.454][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:09.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:09.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:09.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:09.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:09.461][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:09.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:09.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.468][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.469][private$selectFields] biodb.TRACE[2024-06-29 16:03:09.469][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:09.470][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:09.471][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.471][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.472][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.473][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.473][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.474][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.475][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.475][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.476][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.477][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.477][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.478][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.479][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.479][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.480][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.481][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:09.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.490][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [28243]. biodb.DEBUG[2024-06-29 16:03:09.491][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:09.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:09.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:09.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:09.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:09.498][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:09.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:09.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.505][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.506][private$selectFields] biodb.TRACE[2024-06-29 16:03:09.506][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:09.507][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:09.508][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.508][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.509][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.510][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.511][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.511][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.512][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.513][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.513][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.514][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.515][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:09.515][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.516][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.517][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.518][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.518][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:09.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:09.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:09.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:09.528][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [78144]. biodb.DEBUG[2024-06-29 16:03:09.529][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:09.529][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:09.531][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:09.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:09.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:09.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:09.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:09.538][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:09.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:09.540][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.6*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:09.543][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:09.543][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:09.545][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.6%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:03:09.901][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.6%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:03:10.400][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:10.402][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9a13652ab89a613a3b0e10d3b6cb10a0.content" biodb.TRACE[2024-06-29 16:03:10.404][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9a13652ab89a613a3b0e10d3b6cb10a0.request" biodb.DEBUG[2024-06-29 16:03:10.408][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:10.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:10.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:10.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:10.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:10.415][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:10.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:10.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:10.425][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:10.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:10.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:10.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:10.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:10.431][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:10.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:10.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:10.441][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:10.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:10.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:10.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:10.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:10.448][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:10.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:10.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:10.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:10.458][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:10.459][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:10.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:10.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:10.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:10.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:10.466][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:10.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:10.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.473][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.474][private$selectFields] biodb.TRACE[2024-06-29 16:03:10.474][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:10.475][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:10.476][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.477][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.477][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.478][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.479][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.479][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.480][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.481][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.481][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.482][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.483][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.484][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.484][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.485][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.486][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.486][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:10.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.496][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:03:10.496][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:10.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:10.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:10.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:10.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:10.503][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:10.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:10.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.510][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.511][private$selectFields] biodb.TRACE[2024-06-29 16:03:10.512][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:10.512][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:10.513][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.514][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.514][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.515][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.516][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.516][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.517][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.518][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.519][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.519][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.520][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.521][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.521][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.522][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.523][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.523][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:10.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.540][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-06-29 16:03:10.541][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:10.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:10.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:10.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:10.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:10.548][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:10.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:10.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.555][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.556][private$selectFields] biodb.TRACE[2024-06-29 16:03:10.556][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:10.557][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:10.558][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.559][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.559][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.560][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.561][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.561][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.562][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.563][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.563][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.564][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.565][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:10.565][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.566][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.567][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.568][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.568][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:10.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:10.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:10.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:10.578][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-06-29 16:03:10.578][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:10.579][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:10.580][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:10.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:10.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:10.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:10.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:10.587][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:10.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:10.589][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:10.592][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:10.592][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:10.594][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:03:10.938][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:03:11.274][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:11.276][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a985300ab8a01d49254fbf993ad91279.content" biodb.TRACE[2024-06-29 16:03:11.279][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a985300ab8a01d49254fbf993ad91279.request" biodb.DEBUG[2024-06-29 16:03:11.281][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:11.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:11.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:11.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:11.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:11.289][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:11.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:11.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:11.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:11.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:11.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:11.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:11.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:11.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:11.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:11.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:11.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:11.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:11.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:11.299][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:11.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:11.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:11.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:11.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:11.306][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:11.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:11.307][private$loadEntries] Creating entries from ids [1]: "47739". biodb.DEBUG[2024-06-29 16:03:11.308][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:11.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "47739". biodb.TRACE[2024-06-29 16:03:11.310][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:11.311][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:11.312][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:11.312][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:11.313][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:11.314][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:11.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:11.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:11.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:11.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:11.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:11.323][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:11.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:11.324][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=47739". biodb.DEBUG[2024-06-29 16:03:11.326][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:11.327][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:11.328][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=47739". biodb.TRACE[2024-06-29 16:03:11.668][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=47739). biodb.DEBUG[2024-06-29 16:03:12.003][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:12.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0dc9c92acc9df5971b3177a6daad90f3.content" biodb.TRACE[2024-06-29 16:03:12.007][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0dc9c92acc9df5971b3177a6daad90f3.request" biodb.TRACE[2024-06-29 16:03:12.009][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/47739.xml" biodb.DEBUG[2024-06-29 16:03:12.010][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:12.011][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:12.012][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:12.013][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:12.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:12.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:12.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:12.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:12.020][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:12.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:12.022][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.023][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.024][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.025][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.029][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:12.030][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:12.030][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.031][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.032][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:12.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:12.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.035][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:12.036][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:12.037][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.037][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.038][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:12.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:12.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.041][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:12.042][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:12.042][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.043][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:12.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:12.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.047][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:12.048][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:12.049][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.049][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:12.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:12.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.053][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:12.054][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:12.054][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.055][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.056][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:12.057][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:12.058][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.058][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.059][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:12.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:12.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.062][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:12.063][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:12.064][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.064][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:12.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:12.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.068][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:12.069][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:12.069][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.070][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.071][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:12.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:12.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.074][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:12.075][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:12.076][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.076][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.077][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:12.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:12.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.080][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:12.081][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:12.082][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.082][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.083][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:12.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:12.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:12.115][self$createEntryFromContent] Accession numbers: 47739. biodb.TRACE[2024-06-29 16:03:12.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:12.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:12.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:12.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:12.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:12.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:12.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:12.126][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:12.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:12.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:12.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:12.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:12.132][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:12.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:12.134][private$loadEntries] Creating entries from ids [1]: "51744". biodb.DEBUG[2024-06-29 16:03:12.135][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:12.136][cch$loadFileContent] Trying to load 1 files from cache: [1]: "51744". biodb.TRACE[2024-06-29 16:03:12.137][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:12.147][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:12.148][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:12.149][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:12.150][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:12.150][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:12.152][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:12.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:12.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:12.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:12.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:12.159][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:12.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:12.161][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51744". biodb.DEBUG[2024-06-29 16:03:12.162][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:12.163][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:12.164][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51744". biodb.TRACE[2024-06-29 16:03:12.561][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51744). biodb.DEBUG[2024-06-29 16:03:12.897][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:12.899][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/34d89a621633962f5a6b9b09f1ef84ed.content" biodb.TRACE[2024-06-29 16:03:12.901][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/34d89a621633962f5a6b9b09f1ef84ed.request" biodb.TRACE[2024-06-29 16:03:12.903][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/51744.xml" biodb.DEBUG[2024-06-29 16:03:12.904][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:12.905][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:12.906][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:12.907][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:12.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:12.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:12.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:12.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:12.914][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:12.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:12.916][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.917][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.918][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.919][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.922][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:12.923][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:12.924][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.924][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.925][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:12.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:12.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.928][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:12.929][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:12.929][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.930][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.931][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:12.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:12.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.934][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:12.935][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:12.936][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.936][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:12.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:12.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.940][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:12.941][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:12.941][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.942][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:12.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:12.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.946][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:12.947][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:12.947][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.948][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.949][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:12.950][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:12.950][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.951][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.952][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:12.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:12.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.955][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:12.956][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:12.956][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.957][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:12.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:12.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.961][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:12.962][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:12.963][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.963][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:12.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:12.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.967][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:12.968][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:12.969][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.969][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.970][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:12.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:12.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.973][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:12.974][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:12.975][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.975][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.976][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:12.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:12.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:12.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:12.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:12.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:12.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:12.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:13.009][self$createEntryFromContent] Accession numbers: 51744. biodb.TRACE[2024-06-29 16:03:13.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:13.018][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:13.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:13.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:13.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:13.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:13.025][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:13.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:13.027][private$loadEntries] Creating entries from ids [1]: "64473". biodb.DEBUG[2024-06-29 16:03:13.027][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:13.029][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64473". biodb.TRACE[2024-06-29 16:03:13.029][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:13.030][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:13.031][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:13.032][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:13.033][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:13.033][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:13.035][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:13.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:13.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:13.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:13.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:13.042][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:13.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:13.043][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64473". biodb.DEBUG[2024-06-29 16:03:13.046][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:13.046][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:13.047][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64473". biodb.TRACE[2024-06-29 16:03:13.398][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64473). biodb.DEBUG[2024-06-29 16:03:13.741][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:13.742][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0bc75e6e381d0b772364b3d17c4c0f5e.content" biodb.TRACE[2024-06-29 16:03:13.745][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0bc75e6e381d0b772364b3d17c4c0f5e.request" biodb.TRACE[2024-06-29 16:03:13.747][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64473.xml" biodb.DEBUG[2024-06-29 16:03:13.748][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:13.749][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:13.750][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:13.751][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:13.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:13.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:13.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:13.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:13.758][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:13.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:13.760][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.761][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.762][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.762][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.766][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:13.767][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:13.768][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.769][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.770][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:13.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:13.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.772][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:13.773][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:13.774][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.775][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:13.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:13.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.779][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:13.779][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:13.780][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.781][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:13.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:13.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.784][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:13.785][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:13.786][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.786][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:13.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:13.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.790][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:13.791][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:13.792][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.792][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.793][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:13.794][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.795][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.795][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.796][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:13.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.799][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:13.800][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:13.800][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.801][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:13.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:13.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.805][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:13.806][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:13.807][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.808][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:13.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:13.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.812][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:13.812][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:13.813][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.814][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.815][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:13.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:13.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.828][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:13.829][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:13.829][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.830][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:13.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:13.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:13.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:13.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:13.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:13.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:13.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:13.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:13.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:13.862][self$createEntryFromContent] Accession numbers: 64473. biodb.TRACE[2024-06-29 16:03:13.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:13.872][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:13.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:13.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:13.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:13.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:13.878][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:13.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:13.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:13.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:13.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:13.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:13.888][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:13.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:13.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:13.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:13.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:13.894][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:13.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:13.896][private$loadEntries] Creating entries from ids [1]: "75244". biodb.DEBUG[2024-06-29 16:03:13.896][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:13.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75244". biodb.TRACE[2024-06-29 16:03:13.898][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:13.899][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:13.900][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:13.901][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:13.902][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:13.902][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:13.904][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:13.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:13.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:13.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:13.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:13.911][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:13.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:13.912][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75244". biodb.DEBUG[2024-06-29 16:03:13.914][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:13.915][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:13.916][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75244". biodb.TRACE[2024-06-29 16:03:14.262][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75244). biodb.DEBUG[2024-06-29 16:03:14.597][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:14.599][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cae81bf9939177869251c540dee6df85.content" biodb.TRACE[2024-06-29 16:03:14.601][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cae81bf9939177869251c540dee6df85.request" biodb.TRACE[2024-06-29 16:03:14.603][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75244.xml" biodb.DEBUG[2024-06-29 16:03:14.604][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:14.605][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:14.606][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:14.607][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:14.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:14.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:14.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:14.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:14.614][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:14.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:14.616][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:14.617][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:14.618][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.618][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:14.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:14.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.622][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:14.623][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:14.624][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.625][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:14.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:14.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.628][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:14.629][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:14.630][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.630][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.631][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:14.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:14.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.634][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:14.635][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:14.636][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.636][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:14.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:14.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.640][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:14.641][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:14.641][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.642][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:14.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:14.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.646][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:14.646][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:14.647][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.648][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.649][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:14.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:14.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.651][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:14.652][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:14.653][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.654][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.654][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:14.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:14.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.657][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:14.658][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:14.659][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.659][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:14.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:14.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.663][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:14.664][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:14.664][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.665][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.666][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:14.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:14.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.669][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:14.670][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:14.670][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.671][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.672][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:14.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:14.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.675][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:14.675][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:14.676][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.677][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.678][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:14.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:14.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:14.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:14.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:14.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:14.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:14.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:14.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:14.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:14.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:14.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:14.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:14.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:14.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:14.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:14.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:14.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:14.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:14.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:14.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:14.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:14.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:14.709][self$createEntryFromContent] Accession numbers: 75244. biodb.TRACE[2024-06-29 16:03:14.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:14.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:14.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:14.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:14.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:14.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:14.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:14.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:14.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:14.718][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:14.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:14.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:14.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:14.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:14.725][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:14.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:14.726][private$loadEntries] Creating entries from ids [1]: "75311". biodb.DEBUG[2024-06-29 16:03:14.727][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:14.728][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75311". biodb.TRACE[2024-06-29 16:03:14.729][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:14.729][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:14.730][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:14.731][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:14.732][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:14.732][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:14.734][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:14.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:14.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:14.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:14.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:14.741][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:14.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:14.742][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75311". biodb.DEBUG[2024-06-29 16:03:14.752][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:14.752][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:14.753][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75311". biodb.TRACE[2024-06-29 16:03:15.096][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75311). biodb.DEBUG[2024-06-29 16:03:15.436][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:15.437][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4e5c0f0d646c796bdaff17cc90a3658d.content" biodb.TRACE[2024-06-29 16:03:15.440][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4e5c0f0d646c796bdaff17cc90a3658d.request" biodb.TRACE[2024-06-29 16:03:15.442][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75311.xml" biodb.DEBUG[2024-06-29 16:03:15.443][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:15.444][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:15.444][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:15.446][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:15.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:15.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:15.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:15.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:15.452][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:15.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:15.455][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:15.455][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:15.456][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.457][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:15.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:15.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.461][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:15.462][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:15.462][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.463][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.464][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:15.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:15.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.467][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:15.467][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:15.468][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.469][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:15.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:15.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.472][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:15.473][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:15.474][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.474][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.475][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:15.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:15.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.478][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:15.479][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:15.480][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.480][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.481][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:15.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:15.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.484][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:15.485][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:15.485][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.486][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.487][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:15.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:15.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.490][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:15.490][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:15.491][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.492][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.493][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:15.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:15.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.495][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:15.496][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:15.497][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.498][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:15.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:15.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.501][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:15.502][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:15.503][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.503][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:15.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:15.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.507][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:15.508][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:15.509][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.509][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.510][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:15.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:15.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.513][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:15.514][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:15.515][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.515][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.516][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:15.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:15.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:15.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:15.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:15.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:15.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:15.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:15.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:15.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:15.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:15.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:15.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:15.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:15.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:15.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:15.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:15.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:15.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:15.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:15.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:15.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:15.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:15.548][self$createEntryFromContent] Accession numbers: 75311. biodb.TRACE[2024-06-29 16:03:15.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:15.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:15.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:15.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:15.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:15.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:15.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:15.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:15.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:15.557][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:15.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:15.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:15.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:15.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:15.564][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:15.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:15.566][private$loadEntries] Creating entries from ids [1]: "75350". biodb.DEBUG[2024-06-29 16:03:15.566][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:15.567][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75350". biodb.TRACE[2024-06-29 16:03:15.568][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:15.569][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:15.570][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:15.571][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:15.571][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:15.572][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:15.574][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:15.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:15.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:15.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:15.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:15.581][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:15.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:15.582][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75350". biodb.DEBUG[2024-06-29 16:03:15.584][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:15.585][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:15.586][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75350". biodb.TRACE[2024-06-29 16:03:15.964][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75350). biodb.DEBUG[2024-06-29 16:03:16.298][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:16.299][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/37625fe42e340de84bdcc226ef73c285.content" biodb.TRACE[2024-06-29 16:03:16.302][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/37625fe42e340de84bdcc226ef73c285.request" biodb.TRACE[2024-06-29 16:03:16.304][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75350.xml" biodb.DEBUG[2024-06-29 16:03:16.305][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:16.306][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:16.307][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:16.308][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:16.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:16.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:16.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:16.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:16.315][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:16.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:16.317][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:16.318][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:16.318][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.319][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:16.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:16.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.323][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:16.324][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:16.324][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.325][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.326][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:16.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:16.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.329][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:16.330][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:16.330][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.331][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.332][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:16.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:16.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.335][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:16.336][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:16.336][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.337][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:16.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:16.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.341][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:16.341][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:16.342][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.343][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:16.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:16.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.347][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:16.347][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:16.348][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.349][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.350][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:16.350][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:16.351][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.352][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.353][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:16.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:16.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.355][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:16.356][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:16.357][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.358][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:16.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:16.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.361][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:16.362][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:16.363][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.363][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:16.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:16.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.367][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:16.368][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:16.369][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.369][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.370][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:16.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:16.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.373][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:16.374][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:16.375][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.375][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.376][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:16.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:16.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:16.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:16.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:16.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:16.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:16.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:16.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:16.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:16.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:16.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:16.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:16.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:16.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:16.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:16.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:16.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:16.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:16.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:16.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:16.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:16.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:16.422][self$createEntryFromContent] Accession numbers: 75350. biodb.TRACE[2024-06-29 16:03:16.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:16.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:16.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:16.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:16.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:16.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:16.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:16.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:16.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:16.431][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:16.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:16.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:16.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:16.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:16.438][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:16.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:16.440][private$loadEntries] Creating entries from ids [1]: "87236". biodb.DEBUG[2024-06-29 16:03:16.440][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:16.441][cch$loadFileContent] Trying to load 1 files from cache: [1]: "87236". biodb.TRACE[2024-06-29 16:03:16.442][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:16.443][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:16.444][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:16.445][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:16.445][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:16.446][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:16.448][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:16.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:16.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:16.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:16.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:16.454][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:16.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:16.456][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=87236". biodb.DEBUG[2024-06-29 16:03:16.457][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:16.458][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:16.459][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=87236". biodb.TRACE[2024-06-29 16:03:16.799][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=87236). biodb.DEBUG[2024-06-29 16:03:17.133][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:17.134][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/668dc6e1fe28fb2b9645ffb56917cb44.content" biodb.TRACE[2024-06-29 16:03:17.137][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/668dc6e1fe28fb2b9645ffb56917cb44.request" biodb.TRACE[2024-06-29 16:03:17.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/87236.xml" biodb.DEBUG[2024-06-29 16:03:17.140][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:17.141][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:17.142][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:17.143][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:17.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:17.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:17.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:17.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:17.150][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:17.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:17.152][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:17.153][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:17.154][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.154][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:17.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:17.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.158][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:17.159][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:17.160][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.160][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.161][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:17.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:17.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.164][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:17.165][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:17.166][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.166][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.167][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:17.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:17.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.170][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:17.171][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:17.171][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.172][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.173][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:17.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:17.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.176][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:17.177][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:17.177][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.178][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:17.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:17.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.182][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:17.183][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:17.183][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.184][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.185][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:17.186][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:17.186][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.187][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.188][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:17.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:17.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.191][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:17.191][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:17.192][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.193][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:17.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:17.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.197][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:17.197][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:17.198][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.199][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.200][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:17.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:17.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.203][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:17.203][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:17.204][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.205][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.206][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:17.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:17.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.208][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:17.209][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:17.210][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.210][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.211][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:17.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:17.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.213][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:17.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:17.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:17.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:17.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:17.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:17.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:17.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:17.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:17.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:17.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:17.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:17.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:17.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:17.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:17.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:17.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:17.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:17.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:17.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:17.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:17.243][self$createEntryFromContent] Accession numbers: 87236. biodb.TRACE[2024-06-29 16:03:17.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:17.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:17.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:17.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:17.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:17.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:17.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:17.252][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:17.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:17.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:17.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:17.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:17.259][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:17.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:17.260][private$loadEntries] Creating entries from ids [1]: "132193". biodb.DEBUG[2024-06-29 16:03:17.261][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:17.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132193". biodb.TRACE[2024-06-29 16:03:17.263][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:17.264][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:17.265][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:17.266][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:17.266][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:17.267][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:17.269][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:17.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:17.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:17.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:17.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:17.276][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:17.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:17.277][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132193". biodb.DEBUG[2024-06-29 16:03:17.279][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:17.280][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:17.281][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132193". biodb.TRACE[2024-06-29 16:03:17.621][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132193). biodb.DEBUG[2024-06-29 16:03:17.956][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:17.958][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/485d54e768e8b3a26016a2841d39a83c.content" biodb.TRACE[2024-06-29 16:03:17.961][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/485d54e768e8b3a26016a2841d39a83c.request" biodb.TRACE[2024-06-29 16:03:17.962][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132193.xml" biodb.DEBUG[2024-06-29 16:03:17.964][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:17.965][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:17.965][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:17.967][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:17.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:17.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:17.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:17.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:17.973][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:17.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:17.976][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:17.977][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:17.977][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.978][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:17.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:17.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.982][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:17.983][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:17.983][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.984][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.985][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:17.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:17.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:17.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:17.998][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:17.998][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:17.999][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.000][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.001][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:18.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:18.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.004][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:18.004][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:18.005][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.006][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:18.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:18.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.009][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:18.010][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:18.011][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.012][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:18.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:18.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.015][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:18.016][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:18.017][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.017][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.018][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:18.019][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.019][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.020][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.021][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:18.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.024][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:18.024][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:18.025][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.026][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:18.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:18.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.030][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:18.031][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:18.031][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.032][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.033][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:18.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:18.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.036][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:18.037][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:18.038][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.038][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.039][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:18.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:18.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.042][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:18.043][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:18.043][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.044][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.045][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:18.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:18.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:18.076][self$createEntryFromContent] Accession numbers: 132193. biodb.TRACE[2024-06-29 16:03:18.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:18.086][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:18.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:18.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:18.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:18.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:18.092][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:18.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:18.094][private$loadEntries] Creating entries from ids [1]: "146002". biodb.DEBUG[2024-06-29 16:03:18.094][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:18.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "146002". biodb.TRACE[2024-06-29 16:03:18.097][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:18.097][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:18.098][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:18.099][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:18.100][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:18.100][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:18.102][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:18.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:18.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:18.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:18.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:18.109][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:18.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:18.110][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=146002". biodb.DEBUG[2024-06-29 16:03:18.112][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:18.113][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:18.114][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=146002". biodb.TRACE[2024-06-29 16:03:18.454][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=146002). biodb.DEBUG[2024-06-29 16:03:18.790][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:18.792][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f6f6aad2df3f38cd332b2e82fd62eca2.content" biodb.TRACE[2024-06-29 16:03:18.794][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f6f6aad2df3f38cd332b2e82fd62eca2.request" biodb.TRACE[2024-06-29 16:03:18.796][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/146002.xml" biodb.DEBUG[2024-06-29 16:03:18.797][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:18.798][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:18.799][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:18.800][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:18.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:18.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:18.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:18.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:18.807][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:18.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:18.809][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.810][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.810][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.811][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.815][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:18.816][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:18.816][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.817][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.818][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:18.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:18.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.821][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:18.821][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:18.822][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.823][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.824][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:18.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:18.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.827][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:18.827][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:18.828][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.829][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:18.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:18.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.833][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:18.833][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:18.834][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.835][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.836][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:18.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:18.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.838][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:18.839][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:18.840][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.841][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.841][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:18.842][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.843][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.843][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.844][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:18.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.847][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:18.848][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:18.849][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.849][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:18.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:18.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.853][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:18.854][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:18.855][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.855][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:18.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:18.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.859][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:18.860][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:18.861][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.861][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.862][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:18.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:18.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.865][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:18.866][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:18.866][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.867][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.868][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:18.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:18.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:18.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:18.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:18.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:18.900][self$createEntryFromContent] Accession numbers: 146002. biodb.TRACE[2024-06-29 16:03:18.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:18.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:18.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:18.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:18.916][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:18.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:18.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:18.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:18.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:18.923][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:18.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:18.925][private$loadEntries] Creating entries from ids [1]: "65641". biodb.DEBUG[2024-06-29 16:03:18.925][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:18.926][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65641". biodb.TRACE[2024-06-29 16:03:18.927][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:18.928][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:18.929][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:18.930][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:18.931][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:18.931][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:18.933][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:18.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:18.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:18.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:18.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:18.939][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:18.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:18.941][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65641". biodb.DEBUG[2024-06-29 16:03:18.943][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:18.943][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:18.944][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65641". biodb.TRACE[2024-06-29 16:03:19.283][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65641). biodb.DEBUG[2024-06-29 16:03:19.617][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:19.619][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cb3af00d6d6a96efc61a93d5105272fc.content" biodb.TRACE[2024-06-29 16:03:19.621][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cb3af00d6d6a96efc61a93d5105272fc.request" biodb.TRACE[2024-06-29 16:03:19.623][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65641.xml" biodb.DEBUG[2024-06-29 16:03:19.624][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:19.625][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:19.626][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:19.627][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:19.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:19.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:19.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:19.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:19.634][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:19.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:19.636][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:19.637][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:19.638][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.639][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:19.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:19.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.643][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:19.643][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:19.644][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.645][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.646][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:19.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:19.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.649][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:19.650][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:19.650][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.651][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:19.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:19.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.655][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:19.656][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:19.656][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.657][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:19.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:19.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.661][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:19.662][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:19.662][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.663][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:19.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:19.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.667][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:19.667][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:19.668][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.669][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.670][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:19.670][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:19.671][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.672][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.673][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:19.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:19.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.675][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:19.676][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:19.677][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.678][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:19.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:19.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.681][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:19.682][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:19.683][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.683][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:19.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:19.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.687][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:19.688][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:19.689][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.689][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.690][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:19.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:19.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.693][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:19.694][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:19.694][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.695][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.696][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:19.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:19.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:19.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:19.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:19.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:19.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:19.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:19.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:19.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:19.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:19.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:19.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:19.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:19.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:19.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:19.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:19.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:19.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:19.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:19.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:19.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:19.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:19.729][self$createEntryFromContent] Accession numbers: 65641. biodb.TRACE[2024-06-29 16:03:19.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:19.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:19.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:19.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:19.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:19.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:19.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:19.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:19.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:19.739][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:19.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:19.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:19.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:19.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:19.746][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:19.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:19.747][private$loadEntries] Creating entries from ids [1]: "144071". biodb.DEBUG[2024-06-29 16:03:19.748][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:19.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "144071". biodb.TRACE[2024-06-29 16:03:19.750][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:19.751][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:19.752][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:19.752][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:19.753][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:19.754][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:19.756][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:19.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:19.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:19.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:19.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:19.763][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:19.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:19.764][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=144071". biodb.DEBUG[2024-06-29 16:03:19.766][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:19.767][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:19.768][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=144071". biodb.TRACE[2024-06-29 16:03:20.109][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=144071). biodb.DEBUG[2024-06-29 16:03:20.443][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:20.445][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/147c6b10a8e09e725fbbb250103f039d.content" biodb.TRACE[2024-06-29 16:03:20.449][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/147c6b10a8e09e725fbbb250103f039d.request" biodb.TRACE[2024-06-29 16:03:20.451][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/144071.xml" biodb.DEBUG[2024-06-29 16:03:20.453][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:20.454][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:20.455][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:20.457][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:20.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:20.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:20.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:20.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:20.468][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:20.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:20.471][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:20.472][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:20.473][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.474][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:20.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:20.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.479][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:20.479][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:20.480][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.481][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.482][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:20.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:20.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.486][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:20.487][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:20.488][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.488][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:20.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:20.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.494][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:20.495][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:20.495][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.496][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.497][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:20.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:20.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.501][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:20.502][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:20.503][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.504][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:20.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:20.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.508][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:20.509][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:20.510][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.511][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.512][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:20.513][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.514][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.514][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.516][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:20.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.520][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:20.521][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:20.522][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.523][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:20.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:20.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.539][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:20.540][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:20.541][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.543][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:20.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:20.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.548][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:20.550][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:20.551][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.551][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.553][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:20.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:20.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.557][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:20.558][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:20.559][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.560][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.561][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:20.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:20.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:20.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:20.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:20.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:20.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:20.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:20.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:20.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:20.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:20.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:20.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:20.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:20.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:20.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:20.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:20.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:20.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:20.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:20.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:20.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:20.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:20.601][self$createEntryFromContent] Accession numbers: 144071. biodb.TRACE[2024-06-29 16:03:20.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:20.613][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:20.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:20.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:20.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:20.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:20.621][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:20.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:20.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:20.634][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:20.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:20.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:20.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:20.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:20.646][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:20.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:20.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:20.659][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:20.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:20.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:20.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:20.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:20.669][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:20.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:20.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:20.681][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:20.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:20.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:20.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:20.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:20.691][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:20.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:20.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:20.703][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:20.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:20.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:20.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:20.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:20.713][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:20.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:20.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:20.724][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:20.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:20.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:20.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:20.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:20.732][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:20.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:20.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:20.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:20.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:20.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:20.744][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:20.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:20.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:20.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:20.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:20.751][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:20.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:20.753][private$loadEntries] Creating entries from ids [1]: "168650". biodb.DEBUG[2024-06-29 16:03:20.754][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:20.755][cch$loadFileContent] Trying to load 1 files from cache: [1]: "168650". biodb.TRACE[2024-06-29 16:03:20.756][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:20.757][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:20.758][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:20.759][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:20.760][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:20.761][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:20.763][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:20.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:20.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:20.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:20.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:20.770][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:20.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:20.772][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=168650". biodb.DEBUG[2024-06-29 16:03:20.774][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:20.775][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:20.776][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=168650". biodb.TRACE[2024-06-29 16:03:21.122][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=168650). biodb.DEBUG[2024-06-29 16:03:21.464][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:21.466][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fbd7acd341e86313aeb547b3d6d3201b.content" biodb.TRACE[2024-06-29 16:03:21.469][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fbd7acd341e86313aeb547b3d6d3201b.request" biodb.TRACE[2024-06-29 16:03:21.471][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/168650.xml" biodb.DEBUG[2024-06-29 16:03:21.472][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:21.473][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:21.474][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:21.475][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:21.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:21.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:21.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:21.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:21.482][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:21.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:21.484][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:21.485][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:21.486][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.486][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:21.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:21.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.491][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:21.491][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:21.492][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.493][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.494][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:21.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:21.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.496][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:21.497][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:21.498][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.498][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.500][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:21.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:21.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.502][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:21.503][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:21.504][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.504][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:21.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:21.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.508][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:21.509][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:21.510][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.510][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:21.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:21.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.514][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:21.515][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:21.515][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.516][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.517][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:21.518][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.519][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.519][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.520][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:21.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.523][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:21.524][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:21.532][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.533][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:21.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:21.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.537][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:21.538][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:21.539][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.539][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.540][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:21.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:21.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.543][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:21.544][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:21.545][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.545][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.546][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:21.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:21.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.549][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:21.550][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:21.551][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.551][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.552][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:21.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:21.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:21.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:21.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:21.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:21.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:21.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:21.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:21.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:21.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:21.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:21.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:21.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:21.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:21.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:21.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:21.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:21.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:21.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:21.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:21.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:21.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:21.584][self$createEntryFromContent] Accession numbers: 168650. biodb.TRACE[2024-06-29 16:03:21.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:21.593][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:21.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:21.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:21.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:21.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:21.600][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:21.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:21.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:21.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:21.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:21.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:21.610][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:21.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:21.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:21.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:21.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:21.616][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:21.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:21.618][private$loadEntries] Creating entries from ids [1]: "169305". biodb.DEBUG[2024-06-29 16:03:21.619][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:21.620][cch$loadFileContent] Trying to load 1 files from cache: [1]: "169305". biodb.TRACE[2024-06-29 16:03:21.621][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:21.621][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:21.622][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:21.623][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:21.624][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:21.624][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:21.626][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:21.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:21.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:21.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:21.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:21.634][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:21.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:21.635][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169305". biodb.DEBUG[2024-06-29 16:03:21.637][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:21.638][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:21.639][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169305". biodb.TRACE[2024-06-29 16:03:22.017][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169305). biodb.DEBUG[2024-06-29 16:03:22.359][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:22.360][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5eab934e4cfb5514f373385a6170c282.content" biodb.TRACE[2024-06-29 16:03:22.363][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5eab934e4cfb5514f373385a6170c282.request" biodb.TRACE[2024-06-29 16:03:22.365][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/169305.xml" biodb.DEBUG[2024-06-29 16:03:22.366][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:22.367][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:22.368][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:22.369][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:22.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:22.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:22.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:22.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:22.376][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:22.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:22.378][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:22.379][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:22.380][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.380][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:22.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:22.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.384][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:22.385][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:22.386][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.387][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.387][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:22.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:22.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.390][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:22.391][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:22.392][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.393][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.394][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:22.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:22.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.397][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:22.397][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:22.398][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.399][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:22.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:22.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.402][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:22.403][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:22.404][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.404][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:22.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:22.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.408][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:22.409][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:22.410][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.410][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.411][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:22.412][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:22.413][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.413][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.414][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:22.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:22.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.417][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:22.418][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:22.419][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.419][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:22.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:22.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.423][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:22.424][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:22.425][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.425][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:22.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:22.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.430][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:22.430][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:22.431][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.432][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.433][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:22.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:22.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.436][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:22.436][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:22.437][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.438][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.439][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:22.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:22.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:22.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:22.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:22.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:22.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:22.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:22.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:22.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:22.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:22.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:22.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:22.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:22.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:22.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:22.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:22.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:22.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:22.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:22.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:22.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:22.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:22.471][self$createEntryFromContent] Accession numbers: 169305. biodb.TRACE[2024-06-29 16:03:22.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:22.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:22.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:22.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:22.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:22.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:22.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:22.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:22.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:22.480][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:22.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:22.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:22.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:22.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:22.487][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:22.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:22.488][private$loadEntries] Creating entries from ids [1]: "176869". biodb.DEBUG[2024-06-29 16:03:22.489][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:22.490][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176869". biodb.TRACE[2024-06-29 16:03:22.491][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:22.492][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:22.493][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:22.494][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:22.494][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:22.502][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:22.505][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:22.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:22.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:22.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:22.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:22.512][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:22.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:22.513][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176869". biodb.DEBUG[2024-06-29 16:03:22.515][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:22.516][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:22.517][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176869". biodb.TRACE[2024-06-29 16:03:23.068][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176869). biodb.DEBUG[2024-06-29 16:03:23.403][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:23.405][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2c477fa42863c662724815d047e8c32.content" biodb.TRACE[2024-06-29 16:03:23.408][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2c477fa42863c662724815d047e8c32.request" biodb.TRACE[2024-06-29 16:03:23.410][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176869.xml" biodb.DEBUG[2024-06-29 16:03:23.411][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:23.412][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:23.413][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:23.414][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:23.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:23.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:23.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:23.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:23.420][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:23.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:23.423][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:23.423][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:23.424][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.425][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:23.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:23.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.428][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:23.429][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:23.430][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.431][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.431][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:23.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:23.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.434][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:23.435][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:23.436][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.436][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.437][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:23.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:23.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.440][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:23.441][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:23.442][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.442][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:23.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:23.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.446][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:23.447][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:23.447][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.448][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.449][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:23.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:23.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.452][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:23.452][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:23.453][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.454][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.455][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:23.455][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:23.456][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.457][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.458][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:23.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:23.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.461][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:23.461][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:23.462][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.463][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:23.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:23.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.467][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:23.467][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:23.468][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.469][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:23.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:23.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.473][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:23.473][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:23.474][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.475][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.476][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:23.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:23.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.479][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:23.479][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:23.480][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.481][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.481][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:23.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:23.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:23.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:23.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:23.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:23.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:23.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:23.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:23.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:23.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:23.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:23.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:23.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:23.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:23.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:23.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:23.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:23.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:23.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:23.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:23.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:23.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:23.513][self$createEntryFromContent] Accession numbers: 176869. biodb.TRACE[2024-06-29 16:03:23.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:23.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:23.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:23.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:23.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:23.520][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:23.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:23.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:23.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:23.523][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:23.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:23.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:23.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:23.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:23.530][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:23.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:23.532][private$loadEntries] Creating entries from ids [1]: "185696". biodb.DEBUG[2024-06-29 16:03:23.532][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:23.533][cch$loadFileContent] Trying to load 1 files from cache: [1]: "185696". biodb.TRACE[2024-06-29 16:03:23.534][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:23.535][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:23.536][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:23.537][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:23.538][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:23.538][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:23.540][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:23.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:23.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:23.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:23.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:23.547][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:23.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:23.548][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=185696". biodb.DEBUG[2024-06-29 16:03:23.550][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:23.551][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:23.552][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=185696". biodb.TRACE[2024-06-29 16:03:23.893][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=185696). biodb.DEBUG[2024-06-29 16:03:24.227][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:24.229][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/030ac759c83231dbd7b7d6c83788888c.content" biodb.TRACE[2024-06-29 16:03:24.231][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/030ac759c83231dbd7b7d6c83788888c.request" biodb.TRACE[2024-06-29 16:03:24.233][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/185696.xml" biodb.DEBUG[2024-06-29 16:03:24.234][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:24.235][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:24.236][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:24.237][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:24.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:24.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:24.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:24.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:24.244][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:24.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:24.246][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:24.247][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:24.248][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.248][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:24.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:24.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.252][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:24.253][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:24.254][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.254][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.255][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:24.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:24.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.258][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:24.259][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:24.260][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.261][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.262][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:24.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:24.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.264][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:24.265][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:24.266][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.267][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:24.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:24.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.270][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:24.271][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:24.272][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.272][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:24.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:24.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.276][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:24.277][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:24.277][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.278][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.279][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:24.280][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:24.280][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.281][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.282][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:24.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:24.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.285][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:24.286][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:24.286][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.287][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:24.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:24.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.291][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:24.292][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:24.292][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.293][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:24.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:24.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.297][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:24.298][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:24.299][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.299][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.300][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:24.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:24.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.304][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:24.304][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:24.315][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.316][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.317][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:24.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:24.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:24.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:24.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:24.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:24.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:24.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:24.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:24.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:24.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:24.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:24.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:24.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:24.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:24.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:24.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:24.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:24.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:24.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:24.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:24.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:24.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:24.350][self$createEntryFromContent] Accession numbers: 185696. biodb.TRACE[2024-06-29 16:03:24.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:24.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:24.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:24.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:24.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:24.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:24.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:24.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:24.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:24.360][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:24.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:24.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:24.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:24.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:24.367][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:24.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:24.368][private$loadEntries] Creating entries from ids [1]: "190762". biodb.DEBUG[2024-06-29 16:03:24.369][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:24.370][cch$loadFileContent] Trying to load 1 files from cache: [1]: "190762". biodb.TRACE[2024-06-29 16:03:24.371][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:24.372][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:24.372][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:24.373][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:24.374][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:24.375][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:24.377][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:24.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:24.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:24.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:24.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:24.383][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:24.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:24.385][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=190762". biodb.DEBUG[2024-06-29 16:03:24.387][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:24.387][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:24.388][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=190762". biodb.TRACE[2024-06-29 16:03:24.726][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=190762). biodb.DEBUG[2024-06-29 16:03:25.060][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:25.062][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fa9da4de7d7dc0d4458ab1ff7bbbbda0.content" biodb.TRACE[2024-06-29 16:03:25.064][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fa9da4de7d7dc0d4458ab1ff7bbbbda0.request" biodb.TRACE[2024-06-29 16:03:25.066][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/190762.xml" biodb.DEBUG[2024-06-29 16:03:25.067][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:25.068][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:25.069][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:25.070][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:25.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:25.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:25.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:25.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:25.077][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:25.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:25.080][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.080][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.081][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.082][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.086][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:25.086][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:25.087][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.088][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.089][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:25.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:25.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.092][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:25.092][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:25.093][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.094][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.095][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:25.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:25.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.098][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:25.098][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:25.099][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.100][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:25.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:25.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.104][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:25.104][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:25.105][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.106][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:25.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:25.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.109][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:25.110][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:25.111][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.112][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.112][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:25.113][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:25.114][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.115][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.115][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:25.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:25.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.118][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:25.119][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:25.120][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.120][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:25.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:25.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.124][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:25.125][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:25.126][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.126][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:25.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:25.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.130][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:25.131][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:25.132][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.132][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.133][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:25.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:25.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.136][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:25.137][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:25.137][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.138][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.139][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:25.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:25.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:25.170][self$createEntryFromContent] Accession numbers: 190762. biodb.TRACE[2024-06-29 16:03:25.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:25.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:25.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:25.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:25.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:25.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:25.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:25.180][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:25.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:25.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:25.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:25.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:25.187][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:25.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:25.188][private$loadEntries] Creating entries from ids [1]: "193176". biodb.DEBUG[2024-06-29 16:03:25.189][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:25.190][cch$loadFileContent] Trying to load 1 files from cache: [1]: "193176". biodb.TRACE[2024-06-29 16:03:25.191][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:25.192][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:25.192][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:25.193][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:25.194][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:25.195][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:25.197][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:25.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:25.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:25.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:25.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:25.203][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:25.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:25.204][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=193176". biodb.DEBUG[2024-06-29 16:03:25.206][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:25.207][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:25.208][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=193176". biodb.TRACE[2024-06-29 16:03:25.550][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=193176). biodb.DEBUG[2024-06-29 16:03:25.886][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:25.888][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/343c078fd7b00f04bd71e6f2aebb6ed3.content" biodb.TRACE[2024-06-29 16:03:25.890][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/343c078fd7b00f04bd71e6f2aebb6ed3.request" biodb.TRACE[2024-06-29 16:03:25.892][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/193176.xml" biodb.DEBUG[2024-06-29 16:03:25.893][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:25.894][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:25.895][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:25.896][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:25.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:25.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:25.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:25.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:25.903][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:25.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:25.906][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.906][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.917][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.917][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.922][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:25.922][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:25.923][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.924][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.925][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:25.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:25.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.928][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:25.928][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:25.929][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.930][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.931][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:25.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:25.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.934][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:25.934][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:25.935][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.936][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:25.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:25.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.939][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:25.940][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:25.941][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.941][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:25.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:25.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.945][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:25.946][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:25.946][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.947][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.948][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:25.949][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:25.949][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.950][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.951][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:25.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:25.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.954][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:25.954][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:25.955][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.956][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:25.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:25.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.959][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:25.960][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:25.961][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.961][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:25.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:25.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.965][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:25.966][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:25.967][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.967][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.968][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:25.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:25.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.971][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:25.972][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:25.972][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.973][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.974][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:25.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:25.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:25.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:25.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:25.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:25.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:25.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:26.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:26.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:26.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:26.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:26.005][self$createEntryFromContent] Accession numbers: 193176. biodb.TRACE[2024-06-29 16:03:26.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:26.014][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:26.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:26.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:26.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:26.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:26.022][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:26.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:26.023][private$loadEntries] Creating entries from ids [1]: "196395". biodb.DEBUG[2024-06-29 16:03:26.024][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:26.025][cch$loadFileContent] Trying to load 1 files from cache: [1]: "196395". biodb.TRACE[2024-06-29 16:03:26.026][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:26.027][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:26.028][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:26.028][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:26.029][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:26.030][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:26.032][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:26.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:26.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:26.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:26.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:26.039][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:26.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:26.040][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=196395". biodb.DEBUG[2024-06-29 16:03:26.042][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:26.043][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:26.044][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=196395". biodb.TRACE[2024-06-29 16:03:26.388][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=196395). biodb.DEBUG[2024-06-29 16:03:26.721][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:26.723][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/73421bc681b7c5ac1a6297ef414ac513.content" biodb.TRACE[2024-06-29 16:03:26.726][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/73421bc681b7c5ac1a6297ef414ac513.request" biodb.TRACE[2024-06-29 16:03:26.728][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/196395.xml" biodb.DEBUG[2024-06-29 16:03:26.729][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:26.730][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:26.731][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:26.732][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:26.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:26.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:26.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:26.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:26.738][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:26.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:26.741][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:26.742][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:26.742][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.743][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:26.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:26.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.747][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:26.748][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:26.748][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.749][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.750][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:26.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:26.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.753][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:26.754][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:26.754][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.755][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:26.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:26.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.760][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:26.760][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:26.761][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.762][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:26.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:26.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.766][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:26.767][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:26.767][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.768][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.769][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:26.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:26.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.772][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:26.773][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:26.774][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.775][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.776][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:26.776][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.777][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.778][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.779][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:26.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.782][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:26.783][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:26.783][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.784][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:26.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:26.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.788][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:26.789][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:26.790][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.790][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:26.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:26.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.795][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:26.795][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:26.796][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.797][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.798][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:26.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:26.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.800][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:26.801][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:26.802][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.803][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.804][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:26.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:26.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:26.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:26.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:26.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:26.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:26.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:26.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:26.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:26.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:26.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:26.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:26.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:26.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:26.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:26.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:26.844][self$createEntryFromContent] Accession numbers: 196395. biodb.TRACE[2024-06-29 16:03:26.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:26.854][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:26.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:26.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:26.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:26.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:26.861][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:26.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:26.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:26.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:26.871][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:26.872][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:26.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:26.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:26.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:26.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:26.879][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:26.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:26.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.887][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.887][private$selectFields] biodb.TRACE[2024-06-29 16:03:26.888][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:26.889][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:26.889][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.890][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.891][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.891][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.892][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.893][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.894][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.894][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.895][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.896][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.896][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.897][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.898][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.899][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.899][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.900][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:26.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.910][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-06-29 16:03:26.910][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:26.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:26.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:26.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:26.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:26.917][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:26.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:26.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.924][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.925][private$selectFields] biodb.TRACE[2024-06-29 16:03:26.926][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:26.926][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:26.927][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.928][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.928][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.929][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.930][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.930][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.931][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.932][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.933][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.933][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.934][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.935][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.935][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.936][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.937][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.938][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:26.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.947][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-06-29 16:03:26.948][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:26.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:26.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:26.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:26.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:26.955][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:26.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:26.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.962][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.963][private$selectFields] biodb.TRACE[2024-06-29 16:03:26.964][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:26.964][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:26.965][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.966][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.967][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.967][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.968][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.969][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.969][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.970][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.971][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.972][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.972][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:26.973][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.974][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.974][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.975][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.976][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:26.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:26.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:26.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:26.986][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-06-29 16:03:26.986][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:26.987][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:27.003][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.010][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:27.012][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.5*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:27.014][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:27.015][cch$loadFileContent] Trying to load 1 files from cache: [1]: "ebf8c17fa19fb0caf99d83ca8441a2ac". biodb.TRACE[2024-06-29 16:03:27.016][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:27.017][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ebf8c17fa19fb0caf99d83ca8441a2ac.content". biodb.DEBUG[2024-06-29 16:03:27.021][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.028][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.038][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.045][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.056][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.063][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.074][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.080][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.091][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:27.093][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.106][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.113][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.114][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.115][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.116][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.116][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.117][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.118][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.119][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.119][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.120][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.121][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.122][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.122][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.123][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.124][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.124][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.125][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.126][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.126][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.127][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.136][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-06-29 16:03:27.137][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.144][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.150][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.151][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.152][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.152][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.153][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.154][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.155][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.155][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.156][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.157][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.157][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.158][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.159][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.159][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.160][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.161][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.162][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.162][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.163][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.164][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.173][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [8021]. biodb.DEBUG[2024-06-29 16:03:27.174][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.181][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.188][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.188][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.189][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.190][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.190][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.191][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.192][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.193][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.193][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.194][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.195][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.195][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.196][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.197][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.198][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.198][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.199][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.200][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.200][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.201][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.211][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [30382]. biodb.DEBUG[2024-06-29 16:03:27.211][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:27.212][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:27.213][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.220][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:27.223][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.4*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:27.225][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:27.226][cch$loadFileContent] Trying to load 1 files from cache: [1]: "152225e020c3e5947a0f5a90f021cee7". biodb.TRACE[2024-06-29 16:03:27.227][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:27.228][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/152225e020c3e5947a0f5a90f021cee7.content". biodb.DEBUG[2024-06-29 16:03:27.230][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.237][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.247][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.254][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.264][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.270][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.280][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.287][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.297][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.304][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.314][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.320][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.331][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.337][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.354][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:27.355][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.361][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.369][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.369][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.370][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.371][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.371][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.372][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.373][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.373][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.374][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.375][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.376][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.376][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.377][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.378][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.378][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.379][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.380][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.380][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.381][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.382][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.391][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65530]. biodb.DEBUG[2024-06-29 16:03:27.392][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.399][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.406][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.407][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.407][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.408][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.409][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.409][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.410][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.411][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.411][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.412][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.413][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.413][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.414][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.415][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.415][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.416][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.417][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.418][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.418][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.419][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.428][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [90204]. biodb.DEBUG[2024-06-29 16:03:27.429][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.436][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.443][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.444][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.445][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.445][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.446][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.447][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.447][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.448][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.449][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.449][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.450][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.451][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.452][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.452][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.453][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.454][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.454][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.455][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.456][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.456][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.466][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [132793]. biodb.DEBUG[2024-06-29 16:03:27.467][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:27.467][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:27.469][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.475][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:27.478][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:27.480][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:27.481][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9686ce9c957a368dd8f5b4cc9c5b15b3". biodb.TRACE[2024-06-29 16:03:27.482][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:27.483][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9686ce9c957a368dd8f5b4cc9c5b15b3.content". biodb.DEBUG[2024-06-29 16:03:27.485][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.491][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.502][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.508][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.519][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.2*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:27.521][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:27.522][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5d833e77a1be58060d0c3916a1e1b293". biodb.TRACE[2024-06-29 16:03:27.523][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:27.524][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5d833e77a1be58060d0c3916a1e1b293.content". biodb.DEBUG[2024-06-29 16:03:27.526][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.533][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.543][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.550][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.560][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.567][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.577][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:27.578][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.584][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.592][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.593][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.593][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.594][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.600][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.601][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.601][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.602][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.603][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.604][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.605][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.606][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.606][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.607][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.608][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.608][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.609][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.610][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.611][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.611][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.621][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [51836]. biodb.DEBUG[2024-06-29 16:03:27.622][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.629][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.636][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.637][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.638][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.638][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.639][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.640][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.640][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.641][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.642][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.642][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.643][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.644][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.644][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.645][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.646][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.647][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.647][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.648][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.649][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.649][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.659][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [51837]. biodb.DEBUG[2024-06-29 16:03:27.660][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.667][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.674][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.675][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.675][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.676][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.677][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.677][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.678][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.679][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.679][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.680][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.681][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.682][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.682][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.683][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.684][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.685][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.686][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.686][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.687][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.688][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.698][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [132205]. biodb.DEBUG[2024-06-29 16:03:27.699][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:27.699][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:27.716][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.716][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.722][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:27.725][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:27.727][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:27.728][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-06-29 16:03:27.729][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:27.730][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-06-29 16:03:27.731][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.738][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.749][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:27.751][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:27.752][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-06-29 16:03:27.752][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:27.753][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-06-29 16:03:27.755][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.761][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.772][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.778][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.788][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:27.789][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.795][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.803][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.803][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.804][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.805][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.805][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.806][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.807][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.807][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.808][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.809][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.810][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.810][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.811][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.812][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.812][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.813][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.814][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.814][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.815][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.816][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.825][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2024-06-29 16:03:27.826][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.832][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.840][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.840][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.841][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.842][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.842][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.843][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.844][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.845][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.851][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.852][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.853][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.854][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.854][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.855][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.856][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.857][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.857][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.858][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.859][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.859][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.869][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:03:27.869][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.876][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.883][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.883][private$selectFields] biodb.TRACE[2024-06-29 16:03:27.884][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:27.885][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:27.885][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.886][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.887][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.887][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.888][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.889][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.889][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.890][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.891][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.891][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.892][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:27.893][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.894][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.894][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.895][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.896][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:27.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:27.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.905][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2024-06-29 16:03:27.905][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:27.906][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:27.908][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.914][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:27.916][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:27.919][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:27.920][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-06-29 16:03:27.920][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:27.922][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-06-29 16:03:27.923][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.930][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.940][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.946][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.957][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:27.959][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:27.960][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-06-29 16:03:27.961][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:27.962][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-06-29 16:03:27.964][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.971][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.981][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:27.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:27.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:27.988][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:27.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:27.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:27.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:27.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:27.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:27.998][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:27.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:27.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.005][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.015][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:28.016][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.023][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.030][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.031][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.031][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.032][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.033][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.033][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.034][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.035][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.036][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.037][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.038][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.038][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.039][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.040][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.040][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.041][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.042][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.043][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.043][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.044][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.054][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:03:28.055][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.061][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.069][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.070][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.070][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.071][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.072][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.073][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.073][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.074][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.075][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.075][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.076][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.077][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.078][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.078][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.079][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.080][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.081][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.081][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.082][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.083][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.092][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-06-29 16:03:28.093][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.106][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.114][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.114][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.115][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.116][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.116][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.117][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.118][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.119][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.119][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.120][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.121][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.121][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.122][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.123][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.123][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.124][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.125][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.126][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.126][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.127][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.137][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-06-29 16:03:28.137][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:28.138][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:28.139][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.146][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:28.149][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:28.151][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:28.152][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26d0872875c47c33e8205aa7124e0486". biodb.TRACE[2024-06-29 16:03:28.153][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:28.154][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content". biodb.DEBUG[2024-06-29 16:03:28.156][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.163][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.173][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.180][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.190][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.197][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.207][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.214][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.225][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.232][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.243][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.249][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.260][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.267][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.277][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.284][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.296][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:28.298][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:28.299][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-06-29 16:03:28.300][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:28.301][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-06-29 16:03:28.303][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.310][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.320][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.327][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.337][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.338][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.344][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.355][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:28.362][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.369][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.377][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.377][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.378][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.379][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.380][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.380][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.381][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.382][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.382][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.383][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.384][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.385][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.385][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.386][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.387][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.387][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.388][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.389][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.390][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.390][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.400][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-06-29 16:03:28.401][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.407][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.415][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.415][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.416][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.417][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.417][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.418][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.419][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.419][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.420][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.421][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.421][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.422][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.423][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.423][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.424][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.425][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.426][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.426][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.427][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.428][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.437][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-06-29 16:03:28.438][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.445][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.453][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.454][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.454][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.455][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.456][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.457][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.457][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.458][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.459][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.459][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.460][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.461][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.461][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.462][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.463][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.464][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.464][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.465][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.466][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.466][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.475][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.476][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-06-29 16:03:28.477][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:28.477][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:28.495][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.501][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:28.504][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.7*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:28.506][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:28.507][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2b6f29bb7a7663ff23fb5e7dcae5c27f". biodb.TRACE[2024-06-29 16:03:28.508][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:28.509][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2b6f29bb7a7663ff23fb5e7dcae5c27f.content". biodb.DEBUG[2024-06-29 16:03:28.511][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.517][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.528][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.535][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.545][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.551][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.561][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.567][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.577][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.584][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.594][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.601][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.617][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:28.619][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.625][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.632][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.633][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.634][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.634][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.635][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.636][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.636][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.637][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.638][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.638][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.639][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.640][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.640][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.641][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.642][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.642][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.643][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.644][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.644][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.645][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.654][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:03:28.655][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.662][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.669][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.669][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.670][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.671][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.672][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.672][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.673][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.674][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.674][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.675][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.676][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.676][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.677][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.678][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.678][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.679][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.680][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.680][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.681][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.682][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.691][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [28243]. biodb.DEBUG[2024-06-29 16:03:28.692][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.699][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.706][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.707][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.708][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.708][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.709][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.710][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.710][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.711][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.712][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.712][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.713][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.714][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.715][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.715][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.716][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.717][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.717][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.718][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.719][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.719][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.729][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [78144]. biodb.DEBUG[2024-06-29 16:03:28.729][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:28.730][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:28.732][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.738][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:28.741][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.6*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:28.744][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:28.744][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9a13652ab89a613a3b0e10d3b6cb10a0". biodb.TRACE[2024-06-29 16:03:28.745][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:28.746][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9a13652ab89a613a3b0e10d3b6cb10a0.content". biodb.DEBUG[2024-06-29 16:03:28.749][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.756][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.766][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.773][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.783][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.789][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.800][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:28.801][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.807][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.815][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.815][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.816][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.817][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.818][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.818][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.819][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.820][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.820][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.821][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.822][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.822][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.823][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.824][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.825][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.825][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.826][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.827][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.827][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.828][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.837][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:03:28.838][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.845][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.852][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.853][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.854][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.854][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.855][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.861][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.862][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.863][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.864][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.864][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.865][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.866][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.866][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.867][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.868][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.869][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.869][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.870][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.871][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.871][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.880][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-06-29 16:03:28.881][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.888][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.895][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.896][private$selectFields] biodb.TRACE[2024-06-29 16:03:28.896][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:28.897][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:28.898][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.899][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.899][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.900][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.901][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.901][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.902][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.903][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.903][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.904][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.905][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:28.905][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.906][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.907][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.907][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.908][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:28.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:28.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.917][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-06-29 16:03:28.918][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:28.919][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:28.920][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.927][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:28.929][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:28.931][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:28.932][cch$loadFileContent] Trying to load 1 files from cache: [1]: "a985300ab8a01d49254fbf993ad91279". biodb.TRACE[2024-06-29 16:03:28.933][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:28.934][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a985300ab8a01d49254fbf993ad91279.content". biodb.DEBUG[2024-06-29 16:03:28.936][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.943][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.953][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.960][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.970][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.976][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:28.986][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:28.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:28.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:28.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:28.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:28.992][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:28.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:28.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:28.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:28.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:28.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.002][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.008][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.019][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.025][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.035][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.042][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.052][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.058][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.068][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.074][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.084][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.091][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.101][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.114][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.124][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.130][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.140][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.146][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.156][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.162][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.172][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.178][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.188][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.195][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.205][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.211][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.221][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.227][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.237][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.244][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.254][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.260][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.271][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.277][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.287][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.294][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.304][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.310][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.320][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.327][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.337][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.344][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.360][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.367][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.377][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.384][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.394][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.401][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:29.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.411][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:29.412][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.419][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.426][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.426][private$selectFields] biodb.TRACE[2024-06-29 16:03:29.427][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:29.427][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:29.428][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.429][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.430][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.430][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.431][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.432][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.432][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.433][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.434][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.434][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.435][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.436][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.437][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.437][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.438][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.439][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:29.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.448][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-06-29 16:03:29.449][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.455][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.463][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.463][private$selectFields] biodb.TRACE[2024-06-29 16:03:29.464][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:29.465][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:29.466][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.466][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.467][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.468][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.468][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.469][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.470][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.471][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.471][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.472][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.473][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.474][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.474][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.475][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.476][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.476][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:29.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.486][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-06-29 16:03:29.487][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.494][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:29.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.502][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.503][private$selectFields] biodb.TRACE[2024-06-29 16:03:29.503][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:29.504][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:29.505][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.505][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.506][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.507][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.508][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.508][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.509][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.510][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.511][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.511][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.512][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:29.513][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.514][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.514][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.515][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.516][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:29.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:29.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.525][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-06-29 16:03:29.526][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:29.526][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-06-29 16:03:29.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:29.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:29.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:29.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:29.578][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:29.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:29.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:29.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:29.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:29.584][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:29.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:29.587][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:29.589][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:29.590][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:29.591][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:03:29.933][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:03:30.508][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:30.510][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a035d13a630066423fab6713592c5e52.content" biodb.TRACE[2024-06-29 16:03:30.513][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a035d13a630066423fab6713592c5e52.request" biodb.DEBUG[2024-06-29 16:03:30.526][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:30.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:30.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:30.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:30.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:30.533][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:30.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:30.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:30.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:30.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:30.543][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:30.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:30.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:30.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:30.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:30.550][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:30.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:30.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:30.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:30.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:30.560][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:30.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:30.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:30.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:30.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:30.567][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:30.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:30.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:30.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:30.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:30.577][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:30.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:30.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:30.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:30.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:30.583][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:30.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:30.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:30.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:30.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:30.593][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:30.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:30.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:30.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:30.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:30.600][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:30.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:30.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:30.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:30.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:30.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:30.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:30.610][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:30.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:30.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:30.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:30.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:30.617][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:30.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:30.619][private$loadEntries] Creating entries from ids [1]: "9442". biodb.DEBUG[2024-06-29 16:03:30.619][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:30.620][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9442". biodb.TRACE[2024-06-29 16:03:30.621][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:30.622][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:30.623][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:30.624][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:30.625][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:30.625][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:30.627][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:30.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:30.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:30.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:30.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:30.634][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:30.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:30.636][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9442". biodb.DEBUG[2024-06-29 16:03:30.638][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:30.639][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:30.640][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9442". biodb.TRACE[2024-06-29 16:03:30.991][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9442). biodb.DEBUG[2024-06-29 16:03:31.325][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:31.327][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7d1576b26aed79f4c1d758a3f87c749b.content" biodb.TRACE[2024-06-29 16:03:31.330][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7d1576b26aed79f4c1d758a3f87c749b.request" biodb.TRACE[2024-06-29 16:03:31.332][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9442.xml" biodb.DEBUG[2024-06-29 16:03:31.333][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:31.334][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:31.335][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:31.336][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:31.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:31.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:31.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:31.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:31.343][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:31.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:31.345][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:31.346][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:31.347][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.348][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:31.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:31.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.351][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:31.352][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:31.353][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.354][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.354][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:31.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:31.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.357][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:31.358][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:31.359][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.359][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.360][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:31.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:31.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.363][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:31.364][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:31.364][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.365][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:31.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:31.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.369][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:31.370][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:31.370][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.371][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:31.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:31.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.375][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:31.375][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:31.376][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.377][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.378][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:31.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:31.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.380][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:31.381][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:31.382][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.382][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.383][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:31.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:31.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.386][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:31.387][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:31.388][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.388][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:31.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:31.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.392][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:31.393][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:31.394][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.394][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:31.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:31.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.398][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:31.399][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:31.399][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.400][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.401][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:31.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:31.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.404][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:31.405][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:31.405][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.406][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.407][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:31.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:31.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.409][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:31.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:31.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:31.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:31.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:31.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:31.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:31.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:31.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:31.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:31.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:31.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:31.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:31.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:31.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:31.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:31.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:31.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:31.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:31.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:31.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:31.438][self$createEntryFromContent] Accession numbers: 9442. biodb.TRACE[2024-06-29 16:03:31.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:31.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:31.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:31.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:31.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:31.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:31.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:31.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:31.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:31.448][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:31.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:31.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:31.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:31.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:31.463][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:31.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:31.465][private$loadEntries] Creating entries from ids [1]: "34764". biodb.DEBUG[2024-06-29 16:03:31.466][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:31.467][cch$loadFileContent] Trying to load 1 files from cache: [1]: "34764". biodb.TRACE[2024-06-29 16:03:31.468][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:31.469][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:31.469][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:31.470][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:31.471][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:31.472][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:31.473][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:31.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:31.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:31.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:31.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:31.480][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:31.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:31.482][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=34764". biodb.DEBUG[2024-06-29 16:03:31.483][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:31.484][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:31.485][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=34764". biodb.TRACE[2024-06-29 16:03:31.835][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=34764). biodb.DEBUG[2024-06-29 16:03:32.185][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:32.187][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a38508ac0dc37ed2da31f7bda33ae97f.content" biodb.TRACE[2024-06-29 16:03:32.189][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a38508ac0dc37ed2da31f7bda33ae97f.request" biodb.TRACE[2024-06-29 16:03:32.191][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/34764.xml" biodb.DEBUG[2024-06-29 16:03:32.193][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:32.193][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:32.194][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:32.196][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:32.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:32.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:32.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:32.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:32.203][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:32.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:32.205][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:32.206][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:32.206][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.207][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:32.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:32.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.211][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:32.212][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:32.213][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.214][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.215][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:32.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:32.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.217][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:32.218][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:32.219][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.220][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.221][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:32.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:32.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.224][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:32.225][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:32.225][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.226][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:32.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:32.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.230][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:32.231][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:32.231][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.232][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:32.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:32.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.236][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:32.237][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:32.238][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.238][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.239][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:32.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:32.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.242][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:32.243][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:32.244][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.245][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.246][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:32.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:32.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.249][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:32.250][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:32.251][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.251][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:32.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:32.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.255][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:32.256][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:32.257][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.258][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:32.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:32.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.262][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:32.263][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:32.264][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.264][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.265][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:32.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:32.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.269][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:32.269][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:32.270][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.271][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.272][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:32.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:32.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:32.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:32.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:32.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:32.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:32.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:32.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:32.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:32.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:32.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:32.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:32.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:32.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:32.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:32.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:32.305][self$createEntryFromContent] Accession numbers: 34764. biodb.TRACE[2024-06-29 16:03:32.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:32.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:32.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:32.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:32.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:32.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:32.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:32.314][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:32.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:32.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:32.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:32.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:32.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:32.323][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:32.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:32.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.330][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.331][private$selectFields] biodb.TRACE[2024-06-29 16:03:32.332][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:32.333][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:32.333][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.334][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.335][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.335][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.336][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.337][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.338][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.338][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.339][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.340][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.340][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.341][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.342][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.343][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.343][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.344][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:32.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.354][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-06-29 16:03:32.355][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:32.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:32.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:32.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:32.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:32.362][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:32.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:32.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.369][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.370][private$selectFields] biodb.TRACE[2024-06-29 16:03:32.371][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:32.371][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:32.372][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.373][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.373][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.374][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.375][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.376][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.376][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.377][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.378][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.379][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.379][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.380][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.381][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.382][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.383][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.384][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:32.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.394][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-06-29 16:03:32.395][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:32.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:32.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:32.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:32.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:32.402][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:32.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:32.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.437][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.438][private$selectFields] biodb.TRACE[2024-06-29 16:03:32.439][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:32.439][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:32.440][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.441][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.442][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.442][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.443][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.444][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.444][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.445][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.446][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.447][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.447][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:32.448][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.449][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.450][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.450][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.451][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:32.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:32.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:32.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:32.461][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [34764]. biodb.DEBUG[2024-06-29 16:03:32.461][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:32.462][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:32.463][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:32.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:32.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:32.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:32.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:32.470][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:32.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:32.473][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:32.475][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:32.476][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:32.477][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:03:32.937][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:03:33.604][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:33.605][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/365d4ea5e0e90826806fec708da6c9ab.content" biodb.TRACE[2024-06-29 16:03:33.608][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/365d4ea5e0e90826806fec708da6c9ab.request" biodb.DEBUG[2024-06-29 16:03:33.613][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:33.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:33.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:33.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:33.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:33.620][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:33.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:33.621][private$loadEntries] Creating entries from ids [1]: "2535". biodb.DEBUG[2024-06-29 16:03:33.622][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:33.623][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2535". biodb.TRACE[2024-06-29 16:03:33.624][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:33.625][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:33.626][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:33.626][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:33.627][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:33.628][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:33.630][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:33.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:33.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:33.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:33.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:33.637][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:33.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:33.638][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2535". biodb.DEBUG[2024-06-29 16:03:33.640][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:33.641][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:33.642][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2535". biodb.TRACE[2024-06-29 16:03:34.248][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2535). biodb.DEBUG[2024-06-29 16:03:34.584][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:34.586][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e1d9514645c3005d4e4f643b2d18f099.content" biodb.TRACE[2024-06-29 16:03:34.588][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e1d9514645c3005d4e4f643b2d18f099.request" biodb.TRACE[2024-06-29 16:03:34.590][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2535.xml" biodb.DEBUG[2024-06-29 16:03:34.591][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:34.592][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:34.593][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:34.594][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:34.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:34.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:34.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:34.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:34.602][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:34.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:34.604][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:34.605][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:34.605][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.606][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:34.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:34.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.610][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:34.611][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:34.611][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.612][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.613][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:34.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:34.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.616][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:34.617][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:34.617][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.618][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.619][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:34.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:34.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.622][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:34.623][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:34.624][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.624][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.625][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:34.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:34.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.629][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:34.630][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:34.630][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.631][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:34.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:34.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.635][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:34.636][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:34.637][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.638][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.639][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:34.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:34.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.642][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:34.642][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:34.643][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.644][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.645][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:34.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:34.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.648][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.648][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.649][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.650][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.654][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:34.655][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:34.656][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.656][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:34.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:34.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.661][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:34.662][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:34.662][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.663][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.664][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:34.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:34.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.668][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:34.668][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:34.669][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.670][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.671][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:34.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:34.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:34.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:34.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:34.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:34.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:34.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:34.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:34.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:34.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:34.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:34.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:34.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:34.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:34.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:34.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:34.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:34.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:34.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:34.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:34.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:34.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:34.702][self$createEntryFromContent] Accession numbers: 2535. biodb.TRACE[2024-06-29 16:03:34.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:34.712][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:34.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:34.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:34.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:34.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:34.719][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:34.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:34.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:34.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:34.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:34.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:34.729][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:34.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:34.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:34.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:34.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:34.736][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:34.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:34.737][private$loadEntries] Creating entries from ids [1]: "5525". biodb.DEBUG[2024-06-29 16:03:34.738][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:34.739][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5525". biodb.TRACE[2024-06-29 16:03:34.741][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:34.741][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:34.742][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:34.743][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:34.744][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:34.745][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:34.757][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:34.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:34.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:34.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:34.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:34.765][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:34.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:34.766][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=5525". biodb.DEBUG[2024-06-29 16:03:34.768][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:34.769][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:34.770][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=5525". biodb.TRACE[2024-06-29 16:03:35.116][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=5525). biodb.DEBUG[2024-06-29 16:03:35.466][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:35.468][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8c1563abc6b93d34a6b6b66375881583.content" biodb.TRACE[2024-06-29 16:03:35.471][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8c1563abc6b93d34a6b6b66375881583.request" biodb.TRACE[2024-06-29 16:03:35.473][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5525.xml" biodb.DEBUG[2024-06-29 16:03:35.474][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:35.475][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:35.476][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:35.477][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:35.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:35.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:35.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:35.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:35.484][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:35.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:35.487][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:35.487][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:35.488][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.489][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:35.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:35.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.493][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:35.493][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:35.494][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.495][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.495][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:35.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:35.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.498][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:35.499][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:35.500][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.500][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:35.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:35.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.505][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:35.505][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:35.506][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.507][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:35.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:35.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.510][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:35.511][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:35.512][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.513][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:35.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:35.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.517][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:35.518][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:35.518][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.519][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.520][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:35.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:35.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.523][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:35.524][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:35.524][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.525][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.526][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:35.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:35.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.529][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.530][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.531][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.531][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.535][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:35.536][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:35.537][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.538][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:35.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:35.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.542][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:35.542][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:35.543][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.544][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.545][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:35.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:35.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.548][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:35.549][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:35.549][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.550][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.551][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:35.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:35.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:35.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:35.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:35.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:35.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:35.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:35.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:35.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:35.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:35.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:35.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:35.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:35.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:35.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:35.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:35.584][self$createEntryFromContent] Accession numbers: 5525. biodb.TRACE[2024-06-29 16:03:35.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:35.594][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:35.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:35.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:35.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:35.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:35.600][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:35.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:35.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:35.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:35.611][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:35.612][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:35.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:35.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:35.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:35.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:35.619][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:35.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:35.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.626][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.627][private$selectFields] biodb.TRACE[2024-06-29 16:03:35.628][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:35.628][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:35.629][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.630][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.631][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.631][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.632][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.633][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.634][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.634][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.635][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.636][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.636][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.637][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.638][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.639][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.639][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.640][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:35.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.650][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [2535]. biodb.DEBUG[2024-06-29 16:03:35.651][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:35.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:35.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:35.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:35.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:35.657][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:35.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:35.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.665][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.665][private$selectFields] biodb.TRACE[2024-06-29 16:03:35.666][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:35.667][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:35.668][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.668][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.669][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.670][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.671][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.671][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.672][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.673][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.674][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.674][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.675][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.676][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.677][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.677][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.678][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.679][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:35.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.688][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:03:35.689][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:35.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:35.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:35.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:35.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:35.696][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:35.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:35.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.711][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.712][private$selectFields] biodb.TRACE[2024-06-29 16:03:35.713][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:35.713][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:35.714][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.715][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.716][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.717][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.717][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.718][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.719][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.720][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.720][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.721][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.722][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:35.723][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.723][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.724][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.725][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.725][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:35.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:35.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:35.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:35.735][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-06-29 16:03:35.736][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:35.736][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:35.738][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:35.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:35.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:35.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:35.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:35.745][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:35.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:35.747][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=409.9*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:35.749][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:35.750][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:35.751][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=409.9%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:03:36.089][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=409.9%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:03:36.428][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:36.429][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7b0416ab2d5cbf869f248000c039a8e8.content" biodb.TRACE[2024-06-29 16:03:36.432][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7b0416ab2d5cbf869f248000c039a8e8.request" biodb.DEBUG[2024-06-29 16:03:36.434][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:36.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:36.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:36.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:36.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:36.441][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:36.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:36.443][private$loadEntries] Creating entries from ids [1]: "31303". biodb.DEBUG[2024-06-29 16:03:36.444][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:36.445][cch$loadFileContent] Trying to load 1 files from cache: [1]: "31303". biodb.TRACE[2024-06-29 16:03:36.446][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:36.446][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:36.447][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:36.448][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:36.449][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:36.449][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:36.451][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:36.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:36.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:36.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:36.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:36.458][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:36.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:36.460][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=31303". biodb.DEBUG[2024-06-29 16:03:36.461][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:36.462][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:36.463][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=31303". biodb.TRACE[2024-06-29 16:03:36.801][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=31303). biodb.DEBUG[2024-06-29 16:03:37.135][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:37.137][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/99089a071b7e4bcfb0ef9a12b49b39b2.content" biodb.TRACE[2024-06-29 16:03:37.140][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/99089a071b7e4bcfb0ef9a12b49b39b2.request" biodb.TRACE[2024-06-29 16:03:37.142][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/31303.xml" biodb.DEBUG[2024-06-29 16:03:37.143][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:37.144][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:37.145][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:37.146][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:37.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:37.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:37.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:37.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:37.153][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:37.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:37.155][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:37.156][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:37.157][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.157][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:37.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:37.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.161][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:37.162][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:37.163][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.164][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.165][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:37.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:37.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.168][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:37.168][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:37.169][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.170][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.171][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:37.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:37.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.174][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:37.175][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:37.175][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.176][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:37.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:37.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.180][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:37.181][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:37.181][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.182][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:37.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:37.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.186][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:37.187][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:37.187][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.188][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.189][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:37.190][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:37.190][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.191][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.192][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:37.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:37.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.195][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:37.196][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:37.197][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.198][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:37.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:37.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.202][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:37.202][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:37.203][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.204][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:37.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:37.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.208][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:37.209][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:37.209][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.210][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.211][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:37.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:37.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.213][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.214][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:37.215][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:37.215][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.216][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.217][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:37.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:37.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:37.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:37.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:37.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:37.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:37.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:37.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:37.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:37.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:37.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:37.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:37.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:37.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:37.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:37.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:37.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:37.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:37.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:37.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:37.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:37.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:37.249][self$createEntryFromContent] Accession numbers: 31303. biodb.TRACE[2024-06-29 16:03:37.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:37.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:37.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:37.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:37.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:37.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:37.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:37.258][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:37.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:37.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:37.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:37.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:37.265][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:37.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:37.267][private$loadEntries] Creating entries from ids [1]: "37118". biodb.DEBUG[2024-06-29 16:03:37.268][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:37.269][cch$loadFileContent] Trying to load 1 files from cache: [1]: "37118". biodb.TRACE[2024-06-29 16:03:37.270][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:37.270][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:37.271][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:37.272][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:37.273][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:37.274][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:37.276][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:37.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:37.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:37.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:37.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:37.283][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:37.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:37.285][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=37118". biodb.DEBUG[2024-06-29 16:03:37.287][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:37.288][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:37.289][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=37118". biodb.TRACE[2024-06-29 16:03:37.625][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=37118). biodb.DEBUG[2024-06-29 16:03:37.958][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:37.959][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/37e09c6197385dffaf0a241198ec6309.content" biodb.TRACE[2024-06-29 16:03:37.962][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/37e09c6197385dffaf0a241198ec6309.request" biodb.TRACE[2024-06-29 16:03:37.964][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/37118.xml" biodb.DEBUG[2024-06-29 16:03:37.965][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:37.966][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:37.967][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:37.981][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:37.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:37.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:37.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:37.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:37.988][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:37.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:37.990][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:37.991][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:37.992][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.993][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:37.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:37.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:37.997][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:37.997][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:37.998][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:37.999][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.000][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:38.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:38.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.003][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:38.004][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:38.005][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.005][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.006][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:38.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:38.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.009][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:38.010][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:38.011][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.012][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.013][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:38.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:38.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.016][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:38.017][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:38.017][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.018][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:38.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:38.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.022][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:38.023][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:38.024][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.024][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.025][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:38.026][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:38.027][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.028][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.028][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:38.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:38.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.031][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.032][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.033][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.034][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.038][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:38.038][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:38.039][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.040][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:38.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:38.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.044][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:38.044][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:38.045][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.046][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.047][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:38.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:38.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.050][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:38.050][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:38.051][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.052][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.053][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:38.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:38.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:38.085][self$createEntryFromContent] Accession numbers: 37118. biodb.TRACE[2024-06-29 16:03:38.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:38.095][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:38.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:38.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:38.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:38.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:38.102][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:38.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:38.104][private$loadEntries] Creating entries from ids [1]: "39424". biodb.DEBUG[2024-06-29 16:03:38.104][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:38.106][cch$loadFileContent] Trying to load 1 files from cache: [1]: "39424". biodb.TRACE[2024-06-29 16:03:38.106][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:38.107][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:38.108][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:38.109][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:38.110][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:38.110][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:38.112][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:38.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:38.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:38.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:38.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:38.119][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:38.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:38.120][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=39424". biodb.DEBUG[2024-06-29 16:03:38.122][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:38.123][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:38.124][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=39424". biodb.TRACE[2024-06-29 16:03:38.469][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=39424). biodb.DEBUG[2024-06-29 16:03:38.805][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:38.806][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/da5bac251de02a0ce66c3d69c0d59bb8.content" biodb.TRACE[2024-06-29 16:03:38.809][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/da5bac251de02a0ce66c3d69c0d59bb8.request" biodb.TRACE[2024-06-29 16:03:38.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/39424.xml" biodb.DEBUG[2024-06-29 16:03:38.812][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:38.813][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:38.814][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:38.815][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:38.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:38.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:38.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:38.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:38.822][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:38.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:38.825][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.825][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.826][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.827][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.830][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:38.831][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:38.832][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.833][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.833][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:38.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:38.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.836][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:38.837][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:38.838][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.839][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.839][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:38.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:38.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.842][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:38.843][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:38.844][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.844][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:38.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:38.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.848][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:38.849][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:38.850][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.850][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:38.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:38.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.854][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:38.855][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:38.855][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.856][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.857][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:38.858][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:38.858][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.859][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.860][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:38.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:38.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.863][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.864][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.864][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.865][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.869][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:38.869][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:38.870][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.871][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:38.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:38.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.875][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:38.875][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:38.876][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.877][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.877][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:38.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:38.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.880][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:38.881][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:38.882][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.883][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.884][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:38.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:38.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:38.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:38.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:38.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:38.924][self$createEntryFromContent] Accession numbers: 39424. biodb.TRACE[2024-06-29 16:03:38.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:38.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:38.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:38.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:38.933][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:38.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:38.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:38.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:38.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:38.940][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:38.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:38.942][private$loadEntries] Creating entries from ids [1]: "81767". biodb.DEBUG[2024-06-29 16:03:38.943][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:38.944][cch$loadFileContent] Trying to load 1 files from cache: [1]: "81767". biodb.TRACE[2024-06-29 16:03:38.945][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:38.945][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:38.946][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:38.947][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:38.948][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:38.948][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:38.950][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:38.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:38.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:38.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:38.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:38.958][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:38.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:38.960][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=81767". biodb.DEBUG[2024-06-29 16:03:38.962][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:38.963][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:38.964][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=81767". biodb.TRACE[2024-06-29 16:03:39.315][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=81767). biodb.DEBUG[2024-06-29 16:03:39.648][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:39.649][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6d9dc9192959d977e17745ebfa06bb73.content" biodb.TRACE[2024-06-29 16:03:39.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6d9dc9192959d977e17745ebfa06bb73.request" biodb.TRACE[2024-06-29 16:03:39.654][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/81767.xml" biodb.DEBUG[2024-06-29 16:03:39.655][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:39.656][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:39.657][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:39.658][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:39.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:39.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:39.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:39.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:39.665][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:39.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:39.668][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:39.669][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:39.670][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.670][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:39.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:39.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.675][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:39.675][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:39.676][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.677][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.678][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:39.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:39.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.681][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:39.681][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:39.682][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.683][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.684][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:39.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:39.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.687][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:39.687][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:39.688][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.689][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.690][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:39.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:39.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.693][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:39.693][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:39.694][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.695][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:39.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:39.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.698][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:39.699][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:39.700][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.701][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.701][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:39.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:39.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.704][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:39.705][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:39.706][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.706][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.707][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:39.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:39.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.710][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.711][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.712][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.712][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.716][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:39.717][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:39.718][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.718][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:39.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:39.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.722][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:39.723][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:39.724][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.724][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.725][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:39.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:39.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.728][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:39.729][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:39.730][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.730][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.731][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:39.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:39.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:39.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:39.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:39.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:39.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:39.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:39.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:39.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:39.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:39.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:39.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:39.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:39.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:39.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:39.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:39.763][self$createEntryFromContent] Accession numbers: 81767. biodb.TRACE[2024-06-29 16:03:39.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:39.772][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:39.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:39.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:39.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:39.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:39.780][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:39.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:39.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:39.790][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:39.791][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:39.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:39.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:39.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:39.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:39.798][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:39.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:39.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.806][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.807][private$selectFields] biodb.TRACE[2024-06-29 16:03:39.807][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:39.808][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:39.809][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.810][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.810][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.811][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.812][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.812][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.813][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.814][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.815][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.815][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.816][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.817][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.817][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.818][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.819][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.819][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:39.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.829][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [31303]. biodb.DEBUG[2024-06-29 16:03:39.830][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:39.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:39.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:39.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:39.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:39.837][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:39.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:39.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.852][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.853][private$selectFields] biodb.TRACE[2024-06-29 16:03:39.854][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:39.854][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:39.855][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.856][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.856][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.857][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.858][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.859][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.859][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.860][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.861][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.861][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.862][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.863][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.864][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.864][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.865][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.866][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:39.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.875][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [81767]. biodb.DEBUG[2024-06-29 16:03:39.876][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:39.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:39.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:39.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:39.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:39.883][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:39.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:39.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.890][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.890][private$selectFields] biodb.TRACE[2024-06-29 16:03:39.891][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:39.892][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:39.892][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.893][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.894][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.895][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.895][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.896][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.897][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.898][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.898][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.899][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.900][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:39.900][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.901][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.902][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.902][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.903][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:39.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:39.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.913][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [131378]. biodb.DEBUG[2024-06-29 16:03:39.914][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:39.914][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:39.932][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:39.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:39.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:39.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:39.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:39.938][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:39.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:39.941][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:39.943][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:39.944][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-06-29 16:03:39.945][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:39.946][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-06-29 16:03:39.948][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:39.950][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:39.951][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-06-29 16:03:39.952][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:39.953][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-06-29 16:03:39.955][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:39.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:39.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:39.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:39.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:39.962][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:39.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:39.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:39.972][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:39.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:39.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:39.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:39.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:39.979][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:39.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:39.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:39.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:39.989][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:39.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:39.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:39.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:39.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:39.996][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:39.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:39.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:39.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:39.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:40.006][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:40.007][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.014][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.021][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.021][private$selectFields] biodb.TRACE[2024-06-29 16:03:40.022][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:40.023][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:40.023][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.024][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.025][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.026][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.026][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.027][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.028][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.028][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.029][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.030][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.031][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.031][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.032][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.033][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.033][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.034][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:40.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.044][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-06-29 16:03:40.045][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.052][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.059][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.060][private$selectFields] biodb.TRACE[2024-06-29 16:03:40.060][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:40.061][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:40.062][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.063][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.063][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.064][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.065][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.066][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.066][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.067][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.068][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.069][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.069][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.070][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.071][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.071][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.072][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.073][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:40.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.082][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:03:40.083][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.090][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.104][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.105][private$selectFields] biodb.TRACE[2024-06-29 16:03:40.105][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:40.106][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:40.107][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.108][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.108][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.109][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.110][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.110][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.111][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.112][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.113][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.113][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.114][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.115][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.116][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.116][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.117][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.118][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:40.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.127][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-06-29 16:03:40.128][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:40.128][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:40.130][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.136][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:40.139][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:40.141][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:40.142][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7269bbea581f1e243800f8ee4e0f4fdb". biodb.TRACE[2024-06-29 16:03:40.143][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:40.144][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content". biodb.DEBUG[2024-06-29 16:03:40.146][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.152][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:40.162][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.169][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:40.179][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.186][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:40.197][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:40.198][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.205][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.212][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.213][private$selectFields] biodb.TRACE[2024-06-29 16:03:40.213][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:40.214][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:40.215][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.216][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.216][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.217][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.218][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.218][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.219][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.220][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.221][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.221][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.222][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.223][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.223][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.224][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.225][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.226][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:40.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.235][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:03:40.236][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.243][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.250][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.251][private$selectFields] biodb.TRACE[2024-06-29 16:03:40.252][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:40.252][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:40.253][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.254][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.255][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.256][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.256][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.257][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.258][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.258][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.259][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.260][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.260][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.261][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.262][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.263][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.263][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.264][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:40.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.274][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-06-29 16:03:40.274][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.281][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.289][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.290][private$selectFields] biodb.TRACE[2024-06-29 16:03:40.290][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:40.291][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:40.292][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.293][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.293][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.294][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.295][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.295][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.296][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.297][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.298][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.298][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.299][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.300][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.301][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.301][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.302][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.303][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:40.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.312][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-06-29 16:03:40.313][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:40.314][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:40.315][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.322][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:40.325][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:40.327][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:03:40.328][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-06-29 16:03:40.329][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:03:40.330][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-06-29 16:03:40.332][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.341][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:40.357][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.364][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:40.374][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.381][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:40.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:40.391][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:40.392][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.399][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.406][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.406][private$selectFields] biodb.TRACE[2024-06-29 16:03:40.407][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:40.408][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:40.408][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.409][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.410][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.411][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.411][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.412][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.413][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.413][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.414][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.415][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.416][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.416][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.417][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.418][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.418][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.419][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:40.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.429][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-06-29 16:03:40.430][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.437][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.444][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.445][private$selectFields] biodb.TRACE[2024-06-29 16:03:40.446][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:40.446][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:40.447][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.448][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.449][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.449][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.450][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.451][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.452][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.452][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.453][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.454][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.455][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.455][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.456][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.457][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.457][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.458][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:40.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.468][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [64199]. biodb.DEBUG[2024-06-29 16:03:40.469][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.476][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:40.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.483][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.484][private$selectFields] biodb.TRACE[2024-06-29 16:03:40.485][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:40.485][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:40.486][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.487][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.487][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.488][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.489][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.489][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.490][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.491][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.492][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.492][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.493][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:40.494][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.495][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.495][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.496][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.497][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:40.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:40.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:40.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:40.507][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65648]. biodb.DEBUG[2024-06-29 16:03:40.507][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:40.508][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:40.525][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:40.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:40.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:40.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:40.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:40.532][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:40.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:40.534][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:40.537][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:40.537][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:40.539][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:03:40.875][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:03:41.222][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:41.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26eec570aadd234892b573eb0777bd78.content" biodb.TRACE[2024-06-29 16:03:41.227][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26eec570aadd234892b573eb0777bd78.request" biodb.DEBUG[2024-06-29 16:03:41.230][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:41.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:41.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:41.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:41.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:41.237][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:41.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:41.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:41.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:41.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:41.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:41.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:41.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:41.248][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:41.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:41.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:41.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:41.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:41.255][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:41.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:41.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:41.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:41.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:41.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:41.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:41.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:41.266][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:41.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:41.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:41.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:41.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:41.273][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:41.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:41.274][private$loadEntries] Creating entries from ids [1]: "17813". biodb.DEBUG[2024-06-29 16:03:41.275][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:41.276][cch$loadFileContent] Trying to load 1 files from cache: [1]: "17813". biodb.TRACE[2024-06-29 16:03:41.277][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:41.278][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:41.279][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:41.280][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:41.280][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:41.281][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:41.283][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:41.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:41.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:41.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:41.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:41.299][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:41.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:41.301][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17813". biodb.DEBUG[2024-06-29 16:03:41.303][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:41.304][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:41.305][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17813". biodb.TRACE[2024-06-29 16:03:41.693][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17813). biodb.DEBUG[2024-06-29 16:03:42.026][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:42.028][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62f7e1534a05c51cc1431eff021df0bd.content" biodb.TRACE[2024-06-29 16:03:42.031][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62f7e1534a05c51cc1431eff021df0bd.request" biodb.TRACE[2024-06-29 16:03:42.033][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/17813.xml" biodb.DEBUG[2024-06-29 16:03:42.034][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:42.035][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:42.035][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:42.037][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:42.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:42.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:42.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:42.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:42.044][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:42.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:42.046][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:42.047][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:42.048][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.048][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:42.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:42.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.053][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:42.053][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:42.054][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.055][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.056][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:42.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:42.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.059][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:42.059][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:42.060][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.061][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.062][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:42.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:42.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.065][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:42.065][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:42.066][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.067][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.068][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:42.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:42.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.070][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:42.071][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:42.072][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.073][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:42.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:42.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.076][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:42.077][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:42.078][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.078][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.079][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:42.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:42.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.082][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:42.083][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:42.084][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.084][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.085][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:42.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:42.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.088][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:42.089][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:42.089][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.090][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:42.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:42.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.094][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:42.095][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:42.095][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.096][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:42.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:42.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.100][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:42.101][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:42.102][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.102][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.103][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:42.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:42.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.106][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:42.107][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:42.108][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.109][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.109][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:42.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:42.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:42.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:42.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:42.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:42.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:42.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:42.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:42.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:42.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:42.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:42.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:42.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:42.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:42.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:42.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:42.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:42.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:42.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:42.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:42.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:42.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:42.147][self$createEntryFromContent] Accession numbers: 17813. biodb.TRACE[2024-06-29 16:03:42.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:42.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:42.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:42.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:42.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:42.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:42.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:42.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:42.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:42.158][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:42.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:42.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:42.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:42.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:42.165][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:42.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:42.167][private$loadEntries] Creating entries from ids [1]: "30109". biodb.DEBUG[2024-06-29 16:03:42.168][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:42.169][cch$loadFileContent] Trying to load 1 files from cache: [1]: "30109". biodb.TRACE[2024-06-29 16:03:42.170][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:42.171][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:42.172][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:42.173][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:42.174][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:42.175][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:42.177][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:42.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:42.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:42.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:42.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:42.185][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:42.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:42.186][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30109". biodb.DEBUG[2024-06-29 16:03:42.189][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:42.189][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:42.191][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30109". biodb.TRACE[2024-06-29 16:03:42.539][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30109). biodb.DEBUG[2024-06-29 16:03:43.012][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:43.014][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8ed09c4c418a18a426e08dad5ae6a3f9.content" biodb.TRACE[2024-06-29 16:03:43.016][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8ed09c4c418a18a426e08dad5ae6a3f9.request" biodb.TRACE[2024-06-29 16:03:43.018][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/30109.xml" biodb.DEBUG[2024-06-29 16:03:43.020][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:43.021][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:43.021][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:43.023][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:43.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:43.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:43.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:43.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:43.030][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:43.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:43.032][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.033][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.033][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.034][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.038][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:43.039][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:43.040][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.040][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.041][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:43.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:43.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.044][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:43.045][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:43.046][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.046][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.047][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:43.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:43.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.050][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:43.051][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:43.052][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.052][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:43.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:43.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.056][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:43.057][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:43.058][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.058][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:43.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:43.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.062][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:43.063][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:43.063][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.064][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.065][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:43.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:43.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.068][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:43.069][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:43.069][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.070][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.071][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:43.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:43.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.074][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.075][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.075][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.076][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.080][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:43.081][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:43.081][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.082][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:43.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:43.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.086][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:43.087][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:43.087][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.088][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.089][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:43.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:43.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.102][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:43.103][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:43.104][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.105][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.106][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:43.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:43.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:43.137][self$createEntryFromContent] Accession numbers: 30109. biodb.TRACE[2024-06-29 16:03:43.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:43.146][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:43.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:43.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:43.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:43.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:43.153][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:43.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:43.155][private$loadEntries] Creating entries from ids [1]: "33275". biodb.DEBUG[2024-06-29 16:03:43.156][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:43.157][cch$loadFileContent] Trying to load 1 files from cache: [1]: "33275". biodb.TRACE[2024-06-29 16:03:43.158][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:43.158][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:43.159][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:43.160][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:43.161][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:43.161][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:43.163][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:43.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:43.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:43.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:43.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:43.170][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:43.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:43.172][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33275". biodb.DEBUG[2024-06-29 16:03:43.174][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:43.174][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:43.175][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33275". biodb.TRACE[2024-06-29 16:03:43.523][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33275). biodb.DEBUG[2024-06-29 16:03:43.869][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:43.871][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e7b5440dd739854267ce8eafb6ea36b1.content" biodb.TRACE[2024-06-29 16:03:43.873][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e7b5440dd739854267ce8eafb6ea36b1.request" biodb.TRACE[2024-06-29 16:03:43.875][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/33275.xml" biodb.DEBUG[2024-06-29 16:03:43.877][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:43.878][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:43.879][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:43.880][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:43.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:43.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:43.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:43.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:43.887][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:43.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:43.890][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.891][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.891][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.892][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.896][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:43.897][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:43.898][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.899][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.900][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:43.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:43.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.903][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:43.904][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:43.905][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.905][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.906][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:43.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:43.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.910][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:43.910][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:43.911][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.912][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:43.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:43.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.916][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:43.917][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:43.918][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.919][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:43.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:43.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.923][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:43.924][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:43.925][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.925][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.927][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:43.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:43.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.930][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:43.931][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:43.931][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.932][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.933][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:43.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:43.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.936][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.937][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.938][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.939][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.943][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:43.944][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:43.944][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.945][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:43.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:43.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.949][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:43.950][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:43.951][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.952][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.953][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:43.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:43.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.956][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:43.957][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:43.957][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.958][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.959][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:43.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:43.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:43.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:43.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:43.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:43.992][self$createEntryFromContent] Accession numbers: 33275. biodb.TRACE[2024-06-29 16:03:43.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:43.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:43.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:43.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:44.002][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:44.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:44.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:44.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:44.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:44.009][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:44.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:44.011][private$loadEntries] Creating entries from ids [1]: "33277". biodb.DEBUG[2024-06-29 16:03:44.012][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:44.013][cch$loadFileContent] Trying to load 1 files from cache: [1]: "33277". biodb.TRACE[2024-06-29 16:03:44.014][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:44.015][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:44.015][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:44.016][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:44.017][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:44.018][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:44.020][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:44.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:44.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:44.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:44.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:44.027][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:44.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:44.029][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33277". biodb.DEBUG[2024-06-29 16:03:44.031][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:44.032][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:44.033][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33277". biodb.TRACE[2024-06-29 16:03:44.384][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33277). biodb.DEBUG[2024-06-29 16:03:44.726][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:44.727][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9e077bb25f478950bf1d29f1e643c2aa.content" biodb.TRACE[2024-06-29 16:03:44.730][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9e077bb25f478950bf1d29f1e643c2aa.request" biodb.TRACE[2024-06-29 16:03:44.732][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/33277.xml" biodb.DEBUG[2024-06-29 16:03:44.733][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:44.734][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:44.744][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:44.746][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:44.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:44.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:44.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:44.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:44.753][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:44.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:44.756][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:44.756][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:44.757][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.758][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:44.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:44.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.762][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:44.762][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:44.763][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.764][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.765][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:44.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:44.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.768][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:44.768][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:44.769][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.770][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.771][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:44.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:44.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.773][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:44.774][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:44.775][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.776][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:44.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:44.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.779][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:44.780][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:44.781][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.781][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:44.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:44.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.785][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:44.786][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:44.787][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.787][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.788][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:44.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:44.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.791][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:44.792][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:44.793][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.793][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.794][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:44.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:44.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.797][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.798][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.799][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.799][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.803][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:44.804][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:44.804][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.805][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:44.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:44.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.809][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:44.810][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:44.811][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.811][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.812][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:44.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:44.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.816][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:44.816][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:44.817][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.818][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.819][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:44.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:44.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:44.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:44.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:44.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:44.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:44.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:44.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:44.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:44.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:44.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:44.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:44.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:44.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:44.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:44.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:44.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:44.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:44.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:44.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:44.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:44.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:44.852][self$createEntryFromContent] Accession numbers: 33277. biodb.TRACE[2024-06-29 16:03:44.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:44.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:44.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:44.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:44.862][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:44.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:44.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:44.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:44.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:44.869][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:44.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:44.870][private$loadEntries] Creating entries from ids [1]: "52421". biodb.DEBUG[2024-06-29 16:03:44.871][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:44.872][cch$loadFileContent] Trying to load 1 files from cache: [1]: "52421". biodb.TRACE[2024-06-29 16:03:44.873][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:44.874][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:44.875][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:44.876][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:44.876][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:44.877][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:44.879][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:44.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:44.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:44.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:44.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:44.888][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:44.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:44.889][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=52421". biodb.DEBUG[2024-06-29 16:03:44.891][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:44.892][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:44.893][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=52421". biodb.TRACE[2024-06-29 16:03:45.309][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=52421). biodb.DEBUG[2024-06-29 16:03:45.695][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:45.696][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66d999f05cd47f00d9f023cd227b9481.content" biodb.TRACE[2024-06-29 16:03:45.699][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66d999f05cd47f00d9f023cd227b9481.request" biodb.TRACE[2024-06-29 16:03:45.701][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52421.xml" biodb.DEBUG[2024-06-29 16:03:45.702][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:45.704][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:45.705][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:45.706][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:45.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:45.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:45.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:45.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:45.713][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:45.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:45.715][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:45.716][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:45.717][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.717][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:45.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:45.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.722][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:45.722][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:45.723][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.724][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.725][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:45.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:45.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.728][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:45.728][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:45.729][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.730][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.731][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:45.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:45.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.733][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:45.734][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:45.735][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.736][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:45.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:45.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.739][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:45.740][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:45.741][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.742][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:45.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:45.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.746][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:45.747][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:45.747][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.748][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.749][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:45.750][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:45.751][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.752][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.753][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:45.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:45.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.756][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.757][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.757][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.758][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.765][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:45.766][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:45.767][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.767][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:45.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:45.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.771][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:45.772][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:45.773][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.773][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.774][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:45.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:45.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.777][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:45.778][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:45.779][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.779][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.780][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:45.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:45.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:45.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:45.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:45.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:45.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:45.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:45.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:45.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:45.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:45.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:45.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:45.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:45.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:45.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:45.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:45.823][self$createEntryFromContent] Accession numbers: 52421. biodb.TRACE[2024-06-29 16:03:45.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:45.832][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:45.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:45.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:45.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:45.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:45.839][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:45.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:45.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:45.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:45.850][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:03:45.851][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:45.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:45.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:45.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:45.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:45.858][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:45.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:45.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.866][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.867][private$selectFields] biodb.TRACE[2024-06-29 16:03:45.867][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:45.868][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:45.869][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.870][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.870][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.871][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.872][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.872][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.873][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.874][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.875][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.876][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.876][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.877][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.878][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.879][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.879][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.880][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:45.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.891][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-06-29 16:03:45.892][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:45.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:45.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:45.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:45.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:45.899][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:45.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:45.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.906][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.907][private$selectFields] biodb.TRACE[2024-06-29 16:03:45.907][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:45.908][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:45.909][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.910][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.910][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.911][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.912][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.912][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.913][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.914][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.915][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.915][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.916][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.917][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.918][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.918][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.919][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.920][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:45.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.930][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:03:45.930][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:45.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:45.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:45.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:45.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:45.938][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:45.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:45.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.949][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.950][private$selectFields] biodb.TRACE[2024-06-29 16:03:45.951][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:03:45.951][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:03:45.952][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.953][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.954][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.954][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.955][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.956][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.957][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.957][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.958][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.959][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.960][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:03:45.960][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.961][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.962][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.962][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.963][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:03:45.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:45.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:45.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:45.973][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-06-29 16:03:45.973][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:03:45.974][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:03:45.976][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:45.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:45.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:45.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:45.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:45.983][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:45.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:45.985][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.2*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:03:45.988][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:45.989][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:45.990][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.2%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-06-29 16:03:46.364][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.2%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-06-29 16:03:47.261][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:47.263][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/20c224089a82bbffabd2e7dbc67cfae3.content" biodb.TRACE[2024-06-29 16:03:47.267][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/20c224089a82bbffabd2e7dbc67cfae3.request" biodb.DEBUG[2024-06-29 16:03:47.272][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:47.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:47.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:47.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:47.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:47.279][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:47.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:47.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:47.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:47.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:47.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:47.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:47.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:47.290][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:47.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:47.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:47.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:47.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:47.297][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:47.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:47.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:47.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:47.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:47.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:47.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:47.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:47.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:47.307][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:47.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:47.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:47.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:47.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:47.314][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:47.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:47.315][private$loadEntries] Creating entries from ids [1]: "65567". biodb.DEBUG[2024-06-29 16:03:47.316][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:47.317][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65567". biodb.TRACE[2024-06-29 16:03:47.318][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:47.319][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:47.320][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:47.321][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:47.321][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:47.322][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:47.324][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:47.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:47.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:47.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:47.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:47.340][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:47.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:47.342][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65567". biodb.DEBUG[2024-06-29 16:03:47.344][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:47.344][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:47.346][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65567". biodb.TRACE[2024-06-29 16:03:47.698][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65567). biodb.DEBUG[2024-06-29 16:03:50.057][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:50.059][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7f0d7a30f02eb1e897d8c17a3958aa76.content" biodb.TRACE[2024-06-29 16:03:50.062][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7f0d7a30f02eb1e897d8c17a3958aa76.request" biodb.TRACE[2024-06-29 16:03:50.063][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65567.xml" biodb.DEBUG[2024-06-29 16:03:50.065][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:50.065][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:50.066][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:50.067][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:50.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:50.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:50.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:50.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:50.074][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:50.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:50.077][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.078][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.078][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.079][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.083][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:50.083][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:50.084][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.085][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.086][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:50.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:50.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.089][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:50.089][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:50.090][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.091][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:50.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:50.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.094][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:50.095][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:50.096][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.097][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:50.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:50.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.101][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:50.102][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:50.102][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.103][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:50.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:50.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.107][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:50.108][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:50.108][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.109][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.110][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:50.111][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:50.112][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.112][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.113][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:50.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:50.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.116][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.117][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.118][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.119][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.123][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:50.124][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:50.124][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.125][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:50.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:50.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.129][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:50.130][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:50.130][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.131][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.132][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:50.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:50.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.135][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:50.136][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:50.136][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.137][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.138][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:50.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:50.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:50.171][self$createEntryFromContent] Accession numbers: 65567. biodb.TRACE[2024-06-29 16:03:50.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:50.181][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:50.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:50.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:50.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:50.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:50.188][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:50.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:50.190][private$loadEntries] Creating entries from ids [1]: "65576". biodb.DEBUG[2024-06-29 16:03:50.190][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:50.192][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65576". biodb.TRACE[2024-06-29 16:03:50.193][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:50.193][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:50.194][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:50.195][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:50.196][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:50.196][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:50.199][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:50.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:50.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:50.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:50.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:50.207][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:50.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:50.209][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65576". biodb.DEBUG[2024-06-29 16:03:50.211][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:50.211][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:50.212][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65576". biodb.TRACE[2024-06-29 16:03:50.554][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65576). biodb.DEBUG[2024-06-29 16:03:50.888][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:50.890][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/df387492c1d7c1e81f35830307d5d903.content" biodb.TRACE[2024-06-29 16:03:50.892][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/df387492c1d7c1e81f35830307d5d903.request" biodb.TRACE[2024-06-29 16:03:50.894][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65576.xml" biodb.DEBUG[2024-06-29 16:03:50.895][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:50.896][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:50.897][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:50.898][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:50.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:50.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:50.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:50.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:50.905][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:50.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:50.908][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.908][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.909][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.910][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.914][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:50.914][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:50.915][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.916][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.917][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:50.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:50.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.920][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:50.920][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:50.921][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.922][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.923][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:50.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:50.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.926][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:50.927][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:50.928][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.928][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:50.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:50.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.932][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:50.933][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:50.934][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.934][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:50.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:50.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.939][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:50.939][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:50.940][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.941][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.942][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:50.943][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:50.944][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.944][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.945][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:50.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:50.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.948][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.949][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.950][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.950][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:50.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.955][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:50.955][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:50.956][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.957][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:50.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:50.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.961][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:50.962][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:50.963][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.963][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.964][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:50.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:50.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.967][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:50.968][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:50.969][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.980][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.982][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:50.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:50.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:50.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:50.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:50.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:50.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:50.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:51.014][self$createEntryFromContent] Accession numbers: 65576. biodb.TRACE[2024-06-29 16:03:51.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:51.024][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:51.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:51.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:51.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:51.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:51.031][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:51.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:51.032][private$loadEntries] Creating entries from ids [1]: "66352". biodb.DEBUG[2024-06-29 16:03:51.033][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:51.034][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66352". biodb.TRACE[2024-06-29 16:03:51.036][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:51.036][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:51.037][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:51.038][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:51.039][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:51.040][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:51.042][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:51.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:51.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:51.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:51.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:51.049][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:51.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:51.051][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66352". biodb.DEBUG[2024-06-29 16:03:51.053][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:51.053][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:51.055][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66352". biodb.TRACE[2024-06-29 16:03:51.401][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66352). biodb.DEBUG[2024-06-29 16:03:51.739][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:51.740][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/45b0333aa11c1e7eb4af7d2d82f453d6.content" biodb.TRACE[2024-06-29 16:03:51.743][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/45b0333aa11c1e7eb4af7d2d82f453d6.request" biodb.TRACE[2024-06-29 16:03:51.745][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66352.xml" biodb.DEBUG[2024-06-29 16:03:51.746][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:51.747][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:51.748][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:51.749][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:51.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:51.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:51.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:51.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:51.756][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:51.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:51.758][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.759][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.760][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.760][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.764][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:51.765][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:51.766][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.767][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.768][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:51.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:51.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.770][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:51.771][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:51.772][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.773][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:51.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:51.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.777][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:51.777][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:51.778][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.779][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.780][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:51.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:51.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.783][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:51.783][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:51.784][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.785][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:51.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:51.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.789][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:51.789][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:51.790][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.791][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.792][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:51.792][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:51.793][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.794][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.795][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:51.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:51.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.798][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.798][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.799][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.800][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.804][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:51.804][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:51.805][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.806][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:51.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:51.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.810][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:51.810][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:51.811][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.812][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.813][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:51.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:51.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.816][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:51.817][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:51.818][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.818][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.819][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:51.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:51.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:51.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:51.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:51.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:51.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:51.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:51.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:51.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:51.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:51.853][self$createEntryFromContent] Accession numbers: 66352. biodb.TRACE[2024-06-29 16:03:51.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:51.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:51.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:51.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:51.863][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:51.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:51.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:51.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:51.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:51.870][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:51.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:51.872][private$loadEntries] Creating entries from ids [1]: "67567". biodb.DEBUG[2024-06-29 16:03:51.873][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:51.874][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67567". biodb.TRACE[2024-06-29 16:03:51.875][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:51.875][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:51.876][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:51.877][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:51.878][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:51.879][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:51.881][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:51.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:51.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:51.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:51.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:51.888][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:51.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:51.889][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67567". biodb.DEBUG[2024-06-29 16:03:51.891][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:51.892][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:51.893][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67567". biodb.TRACE[2024-06-29 16:03:52.234][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67567). biodb.DEBUG[2024-06-29 16:03:52.569][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:52.570][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ef82f494f4fdd41c2bb93aa0869ad73e.content" biodb.TRACE[2024-06-29 16:03:52.573][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ef82f494f4fdd41c2bb93aa0869ad73e.request" biodb.TRACE[2024-06-29 16:03:52.575][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67567.xml" biodb.DEBUG[2024-06-29 16:03:52.576][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:52.577][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:52.578][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:52.580][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:52.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:52.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:52.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:52.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:52.597][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:52.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:52.600][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:52.601][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:52.602][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.602][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:52.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:52.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.606][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:52.607][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:52.608][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.609][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.609][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:52.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:52.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.613][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:52.613][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:52.614][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.615][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.616][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:52.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:52.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.619][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:52.619][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:52.620][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.621][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:52.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:52.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.625][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:52.625][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:52.626][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.627][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:52.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:52.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.631][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:52.632][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:52.632][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.633][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.634][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:52.634][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:52.635][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.636][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.637][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:52.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:52.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.640][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:52.640][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:52.641][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.642][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:52.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:52.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.646][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:52.647][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:52.647][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.648][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:52.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:52.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.652][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:52.652][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:52.653][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.654][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.655][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:52.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:52.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.658][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:52.659][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:52.659][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.660][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.661][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:52.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:52.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:52.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:52.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:52.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:52.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:52.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:52.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:52.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:52.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:52.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:52.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:52.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:52.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:52.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:52.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:52.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:52.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:52.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:52.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:52.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:52.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:52.694][self$createEntryFromContent] Accession numbers: 67567. biodb.TRACE[2024-06-29 16:03:52.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:52.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:52.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:52.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:52.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:52.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:52.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:52.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:52.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:52.704][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:52.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:52.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:52.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:52.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:52.711][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:52.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:52.713][private$loadEntries] Creating entries from ids [1]: "67693". biodb.DEBUG[2024-06-29 16:03:52.714][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:52.715][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67693". biodb.TRACE[2024-06-29 16:03:52.716][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:52.717][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:52.717][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:52.718][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:52.719][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:52.720][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:52.722][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:52.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:52.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:52.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:52.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:52.729][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:52.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:52.730][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67693". biodb.DEBUG[2024-06-29 16:03:52.732][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:52.733][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:52.734][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67693". biodb.TRACE[2024-06-29 16:03:53.076][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67693). biodb.DEBUG[2024-06-29 16:03:53.650][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:53.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/007181120197262f6a39eff57d7aa092.content" biodb.TRACE[2024-06-29 16:03:53.655][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/007181120197262f6a39eff57d7aa092.request" biodb.TRACE[2024-06-29 16:03:53.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67693.xml" biodb.DEBUG[2024-06-29 16:03:53.658][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:53.659][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:53.660][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:53.661][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:53.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:53.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:53.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:53.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:53.668][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:53.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:53.670][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:53.671][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:53.671][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.672][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:53.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:53.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.676][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:53.677][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:53.677][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.678][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.679][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:53.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:53.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.682][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:53.683][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:53.683][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.684][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.685][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:53.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:53.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.688][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:53.689][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:53.689][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.690][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:53.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:53.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.694][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:53.694][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:53.695][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.696][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:53.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:53.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.700][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:53.701][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:53.701][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.702][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.703][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:53.704][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:53.705][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.705][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.706][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:53.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:53.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.709][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:53.710][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:53.710][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.711][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:53.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:53.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.715][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:53.716][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:53.716][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.717][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:53.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:53.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.721][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:53.722][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:53.722][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.723][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.724][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:53.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:53.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.727][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:53.728][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:53.728][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.729][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.730][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:53.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:53.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:53.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:53.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:53.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:53.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:53.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:53.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:53.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:53.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:53.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:53.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:53.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:53.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:53.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:53.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:53.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:53.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:53.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:53.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:53.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:53.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:53.770][self$createEntryFromContent] Accession numbers: 67693. biodb.TRACE[2024-06-29 16:03:53.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:53.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:53.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:53.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:53.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:53.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:53.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:53.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:53.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:53.780][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:53.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:53.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:53.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:53.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:53.787][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:53.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:53.789][private$loadEntries] Creating entries from ids [1]: "67700". biodb.DEBUG[2024-06-29 16:03:53.789][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:53.791][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67700". biodb.TRACE[2024-06-29 16:03:53.792][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:53.792][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:53.793][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:53.794][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:53.795][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:53.796][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:53.797][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:53.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:53.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:53.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:53.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:53.804][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:53.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:53.806][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67700". biodb.DEBUG[2024-06-29 16:03:53.807][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:53.808][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:53.809][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67700". biodb.TRACE[2024-06-29 16:03:54.151][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67700). biodb.DEBUG[2024-06-29 16:03:54.487][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:54.488][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e41afa9432b74fa2b22a0c53e84c091a.content" biodb.TRACE[2024-06-29 16:03:54.491][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e41afa9432b74fa2b22a0c53e84c091a.request" biodb.TRACE[2024-06-29 16:03:54.493][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67700.xml" biodb.DEBUG[2024-06-29 16:03:54.494][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:54.495][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:54.496][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:54.498][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:54.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:54.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:54.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:54.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:54.505][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:54.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:54.507][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:54.508][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:54.509][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.510][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:54.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:54.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.514][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:54.515][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:54.515][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.516][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.517][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:54.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:54.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.520][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:54.521][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:54.521][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.522][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.523][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:54.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:54.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.526][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:54.527][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:54.527][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.528][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:54.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:54.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.532][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:54.533][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:54.534][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.535][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:54.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:54.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.539][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:54.539][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:54.540][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.541][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.542][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:54.543][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:54.543][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.544][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.545][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:54.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:54.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.548][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:54.549][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:54.550][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.550][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:54.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:54.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.554][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:54.555][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:54.556][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.557][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.558][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:54.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:54.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.561][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:54.561][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:54.562][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.563][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.564][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:54.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:54.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.567][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:54.567][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:54.568][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.569][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.570][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:54.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:54.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:54.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:54.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:54.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:54.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:54.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:54.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:54.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:54.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:54.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:54.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:54.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:54.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:54.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:54.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:54.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:54.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:54.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:54.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:54.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:54.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:54.602][self$createEntryFromContent] Accession numbers: 67700. biodb.TRACE[2024-06-29 16:03:54.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:54.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:54.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:54.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:54.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:54.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:54.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:54.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:54.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:54.611][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:54.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:54.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:54.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:54.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:54.619][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:54.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:54.620][private$loadEntries] Creating entries from ids [1]: "67701". biodb.DEBUG[2024-06-29 16:03:54.621][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:54.622][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67701". biodb.TRACE[2024-06-29 16:03:54.623][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:54.624][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:54.625][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:54.625][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:54.626][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:54.627][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:54.629][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:54.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:54.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:54.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:54.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:54.636][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:54.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:54.638][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67701". biodb.DEBUG[2024-06-29 16:03:54.640][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:54.640][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:54.641][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67701". biodb.TRACE[2024-06-29 16:03:54.995][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67701). biodb.DEBUG[2024-06-29 16:03:55.330][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:55.332][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ca9443fe11bfb8fe207e2797d18dbba3.content" biodb.TRACE[2024-06-29 16:03:55.334][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ca9443fe11bfb8fe207e2797d18dbba3.request" biodb.TRACE[2024-06-29 16:03:55.336][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67701.xml" biodb.DEBUG[2024-06-29 16:03:55.338][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:55.338][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:55.339][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:55.341][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:55.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:55.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:55.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:55.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:55.348][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:55.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:55.350][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:55.351][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:55.351][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.352][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:55.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:55.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.356][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:55.357][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:55.357][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.358][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.359][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:55.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:55.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.362][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:55.363][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:55.363][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.364][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.365][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:55.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:55.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.368][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:55.369][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:55.369][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.380][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:55.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:55.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.385][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:55.386][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:55.387][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.387][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:55.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:55.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.391][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:55.392][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:55.393][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.394][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.394][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:55.395][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:55.396][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.397][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.398][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:55.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:55.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.401][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:55.401][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:55.402][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.403][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:55.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:55.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.406][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:55.407][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:55.408][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.409][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:55.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:55.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.413][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:55.413][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:55.414][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.415][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.416][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:55.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:55.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.418][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:55.419][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:55.420][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.420][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.421][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:55.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:55.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:55.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:55.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:55.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:55.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:55.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:55.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:55.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:55.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:55.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:55.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:55.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:55.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:55.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:55.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:55.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:55.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:55.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:55.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:55.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:55.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:55.453][self$createEntryFromContent] Accession numbers: 67701. biodb.TRACE[2024-06-29 16:03:55.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:55.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:55.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:55.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:55.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:55.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:55.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:55.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:55.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:55.463][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:55.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:55.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:55.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:55.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:55.470][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:55.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:55.471][private$loadEntries] Creating entries from ids [1]: "67705". biodb.DEBUG[2024-06-29 16:03:55.472][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:55.473][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67705". biodb.TRACE[2024-06-29 16:03:55.474][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:55.475][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:55.476][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:55.477][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:55.477][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:55.478][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:55.480][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:55.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:55.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:55.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:55.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:55.487][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:55.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:55.489][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67705". biodb.DEBUG[2024-06-29 16:03:55.491][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:55.492][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:55.493][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67705". biodb.TRACE[2024-06-29 16:03:55.837][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67705). biodb.DEBUG[2024-06-29 16:03:56.177][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:56.179][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/19583a5be2f48ffe4ea86ed642cbc7df.content" biodb.TRACE[2024-06-29 16:03:56.181][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/19583a5be2f48ffe4ea86ed642cbc7df.request" biodb.TRACE[2024-06-29 16:03:56.183][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67705.xml" biodb.DEBUG[2024-06-29 16:03:56.184][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:56.185][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:56.186][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:56.187][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:56.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:56.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:56.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:56.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:56.195][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:56.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:56.197][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:56.198][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:56.198][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.199][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:56.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:56.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.203][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.204][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:56.204][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:56.205][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.206][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.207][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:56.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:56.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.210][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:56.211][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:56.212][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.212][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.213][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:56.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:56.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.216][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:56.217][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:56.218][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.219][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:56.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:56.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.223][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:56.224][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:56.225][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.225][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:56.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:56.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.230][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:56.230][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:56.231][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.232][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.233][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:56.234][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:56.235][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.235][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.236][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:56.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:56.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.239][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:56.240][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:56.241][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.241][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:56.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:56.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.245][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:56.246][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:56.247][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.247][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.249][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:56.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:56.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.251][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:56.252][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:56.253][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.254][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.254][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:56.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:56.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.257][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:56.258][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:56.259][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.260][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.260][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:56.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:56.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:56.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:56.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:56.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:56.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:56.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:56.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:56.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:56.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:56.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:56.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:56.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:56.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:56.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:56.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:56.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:56.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:56.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:56.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:56.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:56.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:56.293][self$createEntryFromContent] Accession numbers: 67705. biodb.TRACE[2024-06-29 16:03:56.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:56.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:56.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:56.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:56.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:56.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:56.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:56.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:56.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:56.302][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:56.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:56.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:56.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:56.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:56.319][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:56.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:56.321][private$loadEntries] Creating entries from ids [1]: "75265". biodb.DEBUG[2024-06-29 16:03:56.321][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:56.323][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75265". biodb.TRACE[2024-06-29 16:03:56.324][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:56.324][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:56.325][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:56.326][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:56.327][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:56.327][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:56.329][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:56.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:56.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:56.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:56.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:56.336][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:56.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:56.338][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75265". biodb.DEBUG[2024-06-29 16:03:56.340][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:56.341][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:56.342][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75265". biodb.TRACE[2024-06-29 16:03:56.686][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75265). biodb.DEBUG[2024-06-29 16:03:57.213][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:57.215][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d89a3a12f8b9f5e8203e72f55b0016ed.content" biodb.TRACE[2024-06-29 16:03:57.218][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d89a3a12f8b9f5e8203e72f55b0016ed.request" biodb.TRACE[2024-06-29 16:03:57.220][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75265.xml" biodb.DEBUG[2024-06-29 16:03:57.221][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:57.222][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:57.223][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:57.224][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:57.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:57.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:57.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:57.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:57.231][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:57.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:57.234][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:57.235][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:57.235][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.236][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:57.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:57.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.240][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:57.241][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:57.241][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.242][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.243][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:57.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:57.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.246][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:57.247][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:57.247][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.248][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.249][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:57.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:57.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.252][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:57.252][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:57.253][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.254][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.255][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:57.256][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:57.256][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.257][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.258][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:57.259][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:57.259][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.260][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.261][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:57.262][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:57.263][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.263][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.264][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:57.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:57.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.267][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:57.268][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:57.269][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.269][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:57.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:57.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.276][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:57.276][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:57.277][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.278][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:57.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:57.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.282][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:57.283][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:57.284][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.284][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.285][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:57.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:57.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.288][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:57.289][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:57.290][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.290][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.291][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:57.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:57.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:57.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:57.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.297][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:57.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:57.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:57.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:57.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:57.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:57.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:57.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:57.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:57.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:57.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:57.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:57.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:57.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:57.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:57.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:57.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:57.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:57.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:57.325][self$createEntryFromContent] Accession numbers: 75265. biodb.TRACE[2024-06-29 16:03:57.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:57.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:57.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:57.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:57.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:57.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:57.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:57.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:57.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:57.335][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:57.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:57.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:57.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:57.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:57.342][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:57.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:57.344][private$loadEntries] Creating entries from ids [1]: "77370". biodb.DEBUG[2024-06-29 16:03:57.345][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:57.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "77370". biodb.TRACE[2024-06-29 16:03:57.347][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:57.347][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:57.348][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:57.349][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:57.350][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:57.350][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:57.352][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:57.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:57.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:57.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:57.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:57.359][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:57.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:57.361][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77370". biodb.DEBUG[2024-06-29 16:03:57.363][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:57.363][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:57.365][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77370". biodb.TRACE[2024-06-29 16:03:57.722][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77370). biodb.DEBUG[2024-06-29 16:03:58.056][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:58.058][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c00fcc12163fc12434466e6319d4b9a8.content" biodb.TRACE[2024-06-29 16:03:58.061][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c00fcc12163fc12434466e6319d4b9a8.request" biodb.TRACE[2024-06-29 16:03:58.063][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/77370.xml" biodb.DEBUG[2024-06-29 16:03:58.064][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:58.065][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:58.066][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:58.067][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:58.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:58.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:58.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:58.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:58.074][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:58.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:58.076][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.077][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.078][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.078][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.082][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:58.083][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:58.084][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.085][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.086][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:58.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:58.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.089][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:58.089][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:58.090][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.091][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:58.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:58.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.095][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:58.095][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:58.096][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.097][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.098][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:58.098][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:58.099][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.100][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.101][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:58.102][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:58.102][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.103][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.104][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:58.105][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:58.105][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.106][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.107][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:58.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:58.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.110][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.111][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.111][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.112][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.116][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:58.117][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:58.118][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.118][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.119][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:58.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:58.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.122][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:58.123][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:58.124][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.124][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.131][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:58.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:58.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.140][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:58.140][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:58.141][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.142][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.143][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:58.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:58.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:58.175][self$createEntryFromContent] Accession numbers: 77370. biodb.TRACE[2024-06-29 16:03:58.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:58.185][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:58.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:58.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:58.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:58.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:58.192][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:58.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:58.193][private$loadEntries] Creating entries from ids [1]: "79074". biodb.DEBUG[2024-06-29 16:03:58.194][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:58.195][cch$loadFileContent] Trying to load 1 files from cache: [1]: "79074". biodb.TRACE[2024-06-29 16:03:58.196][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:58.197][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:58.198][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:58.199][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:58.199][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:58.200][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:58.202][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:58.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:58.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:58.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:58.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:58.209][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:58.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:58.211][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79074". biodb.DEBUG[2024-06-29 16:03:58.213][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:58.214][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:58.215][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79074". biodb.TRACE[2024-06-29 16:03:58.556][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79074). biodb.DEBUG[2024-06-29 16:03:58.901][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:58.903][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9d103521a9057f87b1d7f6dac467847d.content" biodb.TRACE[2024-06-29 16:03:58.905][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9d103521a9057f87b1d7f6dac467847d.request" biodb.TRACE[2024-06-29 16:03:58.907][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/79074.xml" biodb.DEBUG[2024-06-29 16:03:58.908][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:58.909][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:58.910][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:58.911][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:58.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:58.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:58.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:58.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:58.918][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:58.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:58.921][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.921][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.922][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.923][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.927][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:58.928][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:58.929][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.929][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.930][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:58.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:58.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.934][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:58.934][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:58.935][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.936][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.937][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:58.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:58.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.940][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:58.941][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:58.942][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.942][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:58.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:58.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.946][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:58.947][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:58.948][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.949][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:58.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:58.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.953][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:58.953][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:58.954][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.955][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.956][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:58.957][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:58.957][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.958][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.959][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:58.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:58.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.962][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.963][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.964][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.964][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:58.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.968][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:58.969][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:58.970][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.970][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:58.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:58.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.975][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:58.975][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:58.976][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.977][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.978][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:58.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:58.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.981][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:58.982][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:58.983][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.983][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.984][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:58.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:58.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:58.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:58.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:58.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:58.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:58.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:59.017][self$createEntryFromContent] Accession numbers: 79074. biodb.TRACE[2024-06-29 16:03:59.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:59.027][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:59.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:59.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:59.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:59.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:59.034][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:59.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:59.036][private$loadEntries] Creating entries from ids [1]: "79302". biodb.DEBUG[2024-06-29 16:03:59.036][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:59.037][cch$loadFileContent] Trying to load 1 files from cache: [1]: "79302". biodb.TRACE[2024-06-29 16:03:59.038][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:59.039][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:59.040][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:59.041][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:59.042][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:59.042][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:59.044][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:59.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:59.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:59.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:59.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:59.052][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:59.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:59.053][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79302". biodb.DEBUG[2024-06-29 16:03:59.055][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:59.056][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:59.057][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79302". biodb.TRACE[2024-06-29 16:03:59.401][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79302). biodb.DEBUG[2024-06-29 16:03:59.735][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:03:59.737][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/db109891c430ecee6c4d31019e936bb4.content" biodb.TRACE[2024-06-29 16:03:59.740][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/db109891c430ecee6c4d31019e936bb4.request" biodb.TRACE[2024-06-29 16:03:59.742][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/79302.xml" biodb.DEBUG[2024-06-29 16:03:59.743][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:03:59.744][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:03:59.751][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:03:59.757][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:59.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:59.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:59.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:59.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:59.765][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:59.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:03:59.767][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.768][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.768][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.769][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.773][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:59.774][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:59.774][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.775][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.776][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:03:59.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:03:59.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.779][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:59.779][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:59.780][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.781][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:03:59.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:03:59.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.785][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:59.785][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:59.786][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.787][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:03:59.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:03:59.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.791][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:59.792][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:59.792][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.793][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:03:59.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:03:59.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.797][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:59.798][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:03:59.798][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.799][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.800][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:59.801][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:59.802][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.803][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.804][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:03:59.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:03:59.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.807][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.807][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.808][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.809][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.813][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:59.814][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:59.814][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.815][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:03:59.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:03:59.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.819][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:59.820][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:59.821][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.821][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.822][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:03:59.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:03:59.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.825][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:59.826][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:59.827][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.828][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.829][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:03:59.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:03:59.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:59.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:59.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:59.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:59.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:03:59.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:03:59.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:03:59.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:03:59.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:59.862][self$createEntryFromContent] Accession numbers: 79302. biodb.TRACE[2024-06-29 16:03:59.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:03:59.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:03:59.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:03:59.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:03:59.872][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:59.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:59.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:59.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:59.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:59.879][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:59.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:59.881][private$loadEntries] Creating entries from ids [1]: "84164". biodb.DEBUG[2024-06-29 16:03:59.882][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:03:59.883][cch$loadFileContent] Trying to load 1 files from cache: [1]: "84164". biodb.TRACE[2024-06-29 16:03:59.884][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:03:59.885][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:03:59.885][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:03:59.886][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:03:59.887][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:03:59.888][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:03:59.890][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:03:59.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:03:59.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:03:59.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:03:59.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:03:59.897][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:03:59.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:03:59.899][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84164". biodb.DEBUG[2024-06-29 16:03:59.901][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:03:59.901][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:03:59.902][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84164". biodb.TRACE[2024-06-29 16:04:00.243][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84164). biodb.DEBUG[2024-06-29 16:04:00.579][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:00.581][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5878d01d3db7a255abcfdf35c60dd985.content" biodb.TRACE[2024-06-29 16:04:00.583][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5878d01d3db7a255abcfdf35c60dd985.request" biodb.TRACE[2024-06-29 16:04:00.585][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/84164.xml" biodb.DEBUG[2024-06-29 16:04:00.587][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:00.588][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:00.589][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:00.590][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:00.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:00.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:00.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:00.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:00.597][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:00.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:00.599][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:00.600][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:00.601][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.601][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:00.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:00.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.605][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:00.606][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:00.607][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.607][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.608][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:00.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:00.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.611][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:00.612][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:00.613][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.614][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.615][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:00.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:00.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.618][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:00.618][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:00.619][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.620][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:00.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:00.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.624][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:00.624][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:00.625][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.626][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:00.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:00.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.630][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:00.631][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:00.632][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.633][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.634][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:00.635][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:00.636][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.636][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.637][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:00.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:00.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.640][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:00.641][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:00.642][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.642][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:00.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:00.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.646][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:00.647][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:00.648][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.648][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:00.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:00.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.652][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:00.653][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:00.654][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.655][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.655][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:00.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:00.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.658][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:00.659][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:00.660][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.660][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.661][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:00.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:00.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:00.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:00.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:00.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:00.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:00.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:00.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:00.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:00.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:00.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:00.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:00.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:00.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:00.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:00.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:00.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:00.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:00.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:00.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:00.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:00.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:00.704][self$createEntryFromContent] Accession numbers: 84164. biodb.TRACE[2024-06-29 16:04:00.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:00.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:00.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:00.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:00.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:00.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:00.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:00.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:00.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:00.714][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:00.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:00.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:00.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:00.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:00.721][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:00.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:00.723][private$loadEntries] Creating entries from ids [1]: "132314". biodb.DEBUG[2024-06-29 16:04:00.723][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:00.724][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132314". biodb.TRACE[2024-06-29 16:04:00.725][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:00.726][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:00.727][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:00.728][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:00.729][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:00.729][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:00.731][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:00.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:00.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:00.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:00.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:00.739][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:00.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:00.740][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132314". biodb.DEBUG[2024-06-29 16:04:00.742][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:00.743][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:00.744][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132314". biodb.TRACE[2024-06-29 16:04:01.115][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132314). biodb.DEBUG[2024-06-29 16:04:01.453][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:01.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/faff8e4827734119a684907f214879a2.content" biodb.TRACE[2024-06-29 16:04:01.458][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/faff8e4827734119a684907f214879a2.request" biodb.TRACE[2024-06-29 16:04:01.460][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132314.xml" biodb.DEBUG[2024-06-29 16:04:01.461][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:01.462][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:01.462][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:01.464][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:01.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:01.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:01.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:01.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:01.471][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:01.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:01.474][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:01.474][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:01.475][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.476][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:01.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:01.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.480][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:01.481][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:01.482][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.482][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.483][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:01.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:01.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.486][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:01.487][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:01.487][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.488][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.489][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:01.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:01.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.492][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:01.493][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:01.493][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.494][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.495][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:01.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:01.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.498][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:01.499][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:01.499][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.500][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:01.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:01.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.504][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:01.505][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:01.505][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.506][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.507][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:01.508][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:01.508][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.509][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.510][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:01.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:01.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.513][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:01.514][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:01.514][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.515][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:01.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:01.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.519][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:01.520][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:01.521][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.521][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:01.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:01.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.526][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:01.527][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:01.527][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.528][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.529][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:01.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:01.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.532][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:01.533][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:01.534][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.534][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.535][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:01.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:01.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:01.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:01.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:01.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:01.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:01.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:01.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:01.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:01.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:01.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:01.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:01.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:01.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:01.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:01.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:01.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:01.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:01.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:01.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:01.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:01.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:01.570][self$createEntryFromContent] Accession numbers: 132314. biodb.TRACE[2024-06-29 16:04:01.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:01.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:01.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:01.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:01.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:01.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:01.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:01.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:01.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:01.579][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:01.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:01.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:01.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:01.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:01.586][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:01.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:01.588][private$loadEntries] Creating entries from ids [1]: "132338". biodb.DEBUG[2024-06-29 16:04:01.589][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:01.590][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132338". biodb.TRACE[2024-06-29 16:04:01.591][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:01.592][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:01.593][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:01.594][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:01.594][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:01.595][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:01.597][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:01.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:01.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:01.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:01.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:01.605][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:01.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:01.607][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132338". biodb.DEBUG[2024-06-29 16:04:01.609][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:01.610][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:01.611][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132338". biodb.TRACE[2024-06-29 16:04:01.954][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132338). biodb.DEBUG[2024-06-29 16:04:02.289][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:02.291][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ab2b9171a775a690a32a30e73cf2a1c.content" biodb.TRACE[2024-06-29 16:04:02.294][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ab2b9171a775a690a32a30e73cf2a1c.request" biodb.TRACE[2024-06-29 16:04:02.297][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132338.xml" biodb.DEBUG[2024-06-29 16:04:02.298][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:02.299][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:02.300][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:02.301][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:02.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:02.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:02.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:02.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:02.308][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:02.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:02.310][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:02.311][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:02.312][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.313][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:02.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:02.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.316][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.316][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:02.317][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:02.318][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.319][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.319][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:02.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:02.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.338][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:02.339][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:02.340][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.340][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.342][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:02.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:02.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.345][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:02.345][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:02.346][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.347][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:02.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:02.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.351][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:02.352][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:02.352][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.353][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:02.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:02.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.357][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:02.357][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:02.358][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.359][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.360][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:02.360][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:02.361][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.362][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.363][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:02.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:02.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.366][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:02.367][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:02.367][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.368][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:02.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:02.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.372][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:02.373][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:02.374][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.374][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:02.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:02.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.378][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:02.379][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:02.380][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.380][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.381][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:02.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:02.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.385][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:02.386][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:02.386][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.387][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.388][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:02.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:02.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:02.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:02.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:02.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:02.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:02.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:02.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:02.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:02.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:02.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:02.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:02.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:02.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:02.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:02.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:02.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:02.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:02.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:02.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:02.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:02.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:02.422][self$createEntryFromContent] Accession numbers: 132338. biodb.TRACE[2024-06-29 16:04:02.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:02.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:02.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:02.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:02.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:02.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:02.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:02.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:02.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:02.432][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:02.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:02.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:02.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:02.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:02.439][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:02.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:02.441][private$loadEntries] Creating entries from ids [1]: "139019". biodb.DEBUG[2024-06-29 16:04:02.441][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:02.442][cch$loadFileContent] Trying to load 1 files from cache: [1]: "139019". biodb.TRACE[2024-06-29 16:04:02.443][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:02.444][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:02.445][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:02.446][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:02.447][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:02.447][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:02.449][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:02.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:02.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:02.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:02.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:02.456][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:02.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:02.458][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139019". biodb.DEBUG[2024-06-29 16:04:02.460][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:02.461][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:02.462][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139019". biodb.TRACE[2024-06-29 16:04:02.805][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139019). biodb.DEBUG[2024-06-29 16:04:03.140][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:03.142][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c6e6f1783364d5307c1e22caca9f3324.content" biodb.TRACE[2024-06-29 16:04:03.145][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c6e6f1783364d5307c1e22caca9f3324.request" biodb.TRACE[2024-06-29 16:04:03.147][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/139019.xml" biodb.DEBUG[2024-06-29 16:04:03.148][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:03.149][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:03.150][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:03.151][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:03.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:03.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:03.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:03.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:03.159][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:03.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:03.161][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:03.162][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:03.163][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.163][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:03.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:03.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.168][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:03.168][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:03.169][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.170][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.171][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:03.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:03.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.174][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:03.175][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:03.175][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.176][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.177][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:03.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:03.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.180][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:03.181][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:03.182][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.183][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:03.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:03.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.187][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:03.187][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:03.188][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.189][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:03.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:03.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.193][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:03.194][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:03.195][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.196][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.197][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:03.198][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:03.198][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.199][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.200][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:03.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:03.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.203][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:03.204][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:03.205][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.205][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:03.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:03.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.209][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:03.210][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:03.211][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.212][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:03.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:03.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.216][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:03.216][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:03.217][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.218][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.219][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:03.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:03.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.222][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:03.223][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:03.224][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.224][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.225][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:03.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:03.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:03.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:03.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:03.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:03.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:03.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:03.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:03.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:03.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:03.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:03.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:03.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:03.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:03.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:03.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:03.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:03.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:03.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:03.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:03.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:03.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:03.258][self$createEntryFromContent] Accession numbers: 139019. biodb.TRACE[2024-06-29 16:04:03.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:03.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:03.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:03.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:03.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:03.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:03.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:03.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:03.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:03.277][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:03.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:03.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:03.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:03.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:03.285][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:03.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:03.287][private$loadEntries] Creating entries from ids [1]: "139367". biodb.DEBUG[2024-06-29 16:04:03.287][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:03.289][cch$loadFileContent] Trying to load 1 files from cache: [1]: "139367". biodb.TRACE[2024-06-29 16:04:03.290][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:03.290][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:03.291][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:03.292][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:03.293][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:03.293][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:03.295][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:03.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:03.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:03.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:03.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:03.302][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:03.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:03.304][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139367". biodb.DEBUG[2024-06-29 16:04:03.306][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:03.307][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:03.308][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139367". biodb.TRACE[2024-06-29 16:04:03.650][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139367). biodb.DEBUG[2024-06-29 16:04:03.983][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:03.985][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ad7d38680a9a89d96fe967aa23d4180d.content" biodb.TRACE[2024-06-29 16:04:03.987][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ad7d38680a9a89d96fe967aa23d4180d.request" biodb.TRACE[2024-06-29 16:04:03.989][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/139367.xml" biodb.DEBUG[2024-06-29 16:04:03.991][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:03.991][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:03.992][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:03.993][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:03.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:03.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:03.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:04.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:04.001][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:04.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:04.003][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:04.004][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:04.004][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.005][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:04.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:04.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.009][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:04.010][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:04.011][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.011][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.012][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:04.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:04.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.015][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:04.016][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:04.017][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.017][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:04.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:04.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.021][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:04.022][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:04.023][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.024][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:04.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:04.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.028][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:04.029][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:04.029][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.030][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.031][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:04.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:04.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.034][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:04.035][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:04.035][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.036][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.037][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:04.038][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:04.038][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.039][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.040][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:04.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:04.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.043][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.044][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.045][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.046][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.050][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:04.050][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:04.051][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.052][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.053][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:04.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:04.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.056][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:04.057][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:04.057][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.058][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.059][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:04.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:04.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.062][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:04.063][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:04.064][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.065][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.066][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:04.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:04.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:04.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:04.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:04.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:04.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:04.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:04.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:04.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:04.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:04.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:04.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:04.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:04.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:04.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:04.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:04.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:04.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:04.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:04.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:04.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:04.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:04.099][self$createEntryFromContent] Accession numbers: 139367. biodb.TRACE[2024-06-29 16:04:04.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:04.108][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:04.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:04.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:04.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:04.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:04.116][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:04.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:04.118][private$loadEntries] Creating entries from ids [1]: "145029". biodb.DEBUG[2024-06-29 16:04:04.118][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:04.120][cch$loadFileContent] Trying to load 1 files from cache: [1]: "145029". biodb.TRACE[2024-06-29 16:04:04.121][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:04.122][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:04.122][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:04.123][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:04.124][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:04.125][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:04.127][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:04.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:04.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:04.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:04.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:04.134][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:04.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:04.136][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=145029". biodb.DEBUG[2024-06-29 16:04:04.138][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:04.138][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:04.139][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=145029". biodb.TRACE[2024-06-29 16:04:04.487][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=145029). biodb.DEBUG[2024-06-29 16:04:04.901][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:04.903][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6db4642c7bdbd10dc105b3470394caa5.content" biodb.TRACE[2024-06-29 16:04:04.905][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6db4642c7bdbd10dc105b3470394caa5.request" biodb.TRACE[2024-06-29 16:04:04.908][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/145029.xml" biodb.DEBUG[2024-06-29 16:04:04.909][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:04.910][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:04.911][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:04.912][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:04.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:04.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:04.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:04.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:04.919][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:04.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:04.922][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:04.922][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:04.923][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.924][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:04.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:04.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.928][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:04.929][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:04.930][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.930][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.931][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:04.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:04.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.934][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:04.935][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:04.936][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.936][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.937][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:04.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:04.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.941][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:04.941][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:04.942][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.943][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.944][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:04.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:04.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.947][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:04.947][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:04.948][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.949][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:04.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:04.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.953][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:04.954][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:04.954][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.955][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.956][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:04.957][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:04.957][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.958][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.959][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:04.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:04.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.973][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.974][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.975][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.976][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:04.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.980][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:04.981][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:04.981][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.982][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:04.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:04.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.986][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:04.987][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:04.988][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.988][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.989][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:04.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:04.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.992][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:04.993][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:04.993][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.994][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.995][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:04.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:04.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:04.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:04.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:04.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:05.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:05.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:05.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:05.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:05.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:05.028][self$createEntryFromContent] Accession numbers: 145029. biodb.TRACE[2024-06-29 16:04:05.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:05.037][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:05.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:05.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:05.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:05.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:05.044][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:05.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:05.046][private$loadEntries] Creating entries from ids [1]: "173077". biodb.DEBUG[2024-06-29 16:04:05.047][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:05.048][cch$loadFileContent] Trying to load 1 files from cache: [1]: "173077". biodb.TRACE[2024-06-29 16:04:05.049][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:05.050][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:05.050][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:05.051][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:05.052][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:05.053][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:05.055][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:05.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:05.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:05.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:05.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:05.062][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:05.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:05.064][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=173077". biodb.DEBUG[2024-06-29 16:04:05.066][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:05.066][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:05.067][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=173077". biodb.TRACE[2024-06-29 16:04:05.416][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=173077). biodb.DEBUG[2024-06-29 16:04:05.828][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:05.830][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/337fedbe654250105ac3b03683794b9b.content" biodb.TRACE[2024-06-29 16:04:05.832][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/337fedbe654250105ac3b03683794b9b.request" biodb.TRACE[2024-06-29 16:04:05.834][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/173077.xml" biodb.DEBUG[2024-06-29 16:04:05.836][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:05.836][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:05.837][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:05.839][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:05.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:05.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:05.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:05.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:05.846][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:05.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:05.848][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.849][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.850][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.850][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.854][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:05.855][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:05.856][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.857][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:05.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:05.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.860][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:05.861][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:05.862][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.863][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.863][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:05.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:05.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.866][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:05.867][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:05.868][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.869][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:05.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:05.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.872][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:05.873][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:05.874][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.875][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:05.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:05.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.878][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:05.879][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:05.880][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.881][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.881][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:05.882][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:05.883][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.884][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.885][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:05.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:05.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.887][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.888][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.889][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.890][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.893][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:05.894][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:05.895][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.896][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:05.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:05.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.899][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:05.900][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:05.901][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.902][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.902][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:05.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:05.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.905][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:05.906][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:05.907][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.908][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.909][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:05.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:05.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:05.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:05.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:05.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:05.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:05.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:05.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:05.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:05.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:05.941][self$createEntryFromContent] Accession numbers: 173077. biodb.TRACE[2024-06-29 16:04:05.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:05.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:05.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:05.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:05.950][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:05.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:05.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:05.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:05.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:05.958][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:05.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:05.959][private$loadEntries] Creating entries from ids [1]: "365445". biodb.DEBUG[2024-06-29 16:04:05.960][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:05.961][cch$loadFileContent] Trying to load 1 files from cache: [1]: "365445". biodb.TRACE[2024-06-29 16:04:05.962][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:05.963][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:05.964][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:05.964][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:05.965][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:05.966][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:05.968][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:05.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:05.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:05.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:05.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:05.983][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:05.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:05.985][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=365445". biodb.DEBUG[2024-06-29 16:04:05.988][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:05.988][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:05.989][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=365445". biodb.TRACE[2024-06-29 16:04:06.349][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=365445). biodb.DEBUG[2024-06-29 16:04:06.686][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:06.688][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/026ecb4be6491f40bcefe5cdf8425328.content" biodb.TRACE[2024-06-29 16:04:06.691][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/026ecb4be6491f40bcefe5cdf8425328.request" biodb.TRACE[2024-06-29 16:04:06.693][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/365445.xml" biodb.DEBUG[2024-06-29 16:04:06.694][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:06.695][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:06.696][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:06.697][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:06.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:06.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:06.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:06.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:06.704][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:06.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:06.707][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:06.708][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:06.708][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.709][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:06.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:06.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.713][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:06.714][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:06.714][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.715][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.716][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:06.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:06.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.718][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.719][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:06.720][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:06.721][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.721][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.722][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:06.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:06.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.725][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:06.726][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:06.727][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.728][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:06.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:06.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.732][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:06.733][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:06.733][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.734][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:06.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:06.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.738][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:06.739][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:06.740][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.740][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.741][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:06.742][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:06.743][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.744][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.745][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:06.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:06.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.748][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:06.749][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:06.749][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.750][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:06.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:06.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.754][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:06.755][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:06.756][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.756][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:06.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:06.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.761][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:06.761][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:06.762][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.763][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.764][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:06.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:06.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.767][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:06.768][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:06.769][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.769][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.770][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:06.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:06.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:06.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:06.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:06.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:06.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:06.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:06.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:06.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:06.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:06.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:06.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:06.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:06.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:06.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:06.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:06.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:06.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:06.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:06.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:06.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:06.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:06.805][self$createEntryFromContent] Accession numbers: 365445. biodb.TRACE[2024-06-29 16:04:06.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:06.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:06.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:06.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:06.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:06.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:06.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:06.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:06.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:06.815][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:06.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:06.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:06.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:06.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:06.822][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:06.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:06.824][private$loadEntries] Creating entries from ids [1]: "32151". biodb.DEBUG[2024-06-29 16:04:06.824][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:06.826][cch$loadFileContent] Trying to load 1 files from cache: [1]: "32151". biodb.TRACE[2024-06-29 16:04:06.826][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:06.827][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:06.828][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:06.829][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:06.830][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:06.831][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:06.833][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:06.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:06.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:06.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:06.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:06.840][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:06.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:06.841][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=32151". biodb.DEBUG[2024-06-29 16:04:06.843][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:06.844][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:06.845][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=32151". biodb.TRACE[2024-06-29 16:04:07.231][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=32151). biodb.DEBUG[2024-06-29 16:04:07.573][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:07.575][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/094c4c16dd654c0e11594a0cd5a42217.content" biodb.TRACE[2024-06-29 16:04:07.578][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/094c4c16dd654c0e11594a0cd5a42217.request" biodb.TRACE[2024-06-29 16:04:07.579][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32151.xml" biodb.DEBUG[2024-06-29 16:04:07.581][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:07.582][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:07.582][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:07.584][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:07.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:07.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:07.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:07.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:07.591][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:07.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:07.593][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:07.594][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:07.595][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.595][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:07.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:07.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.599][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:07.600][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:07.601][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.601][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.602][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:07.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:07.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.605][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:07.606][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:07.607][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.607][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.608][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:07.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:07.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.611][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:07.612][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:07.613][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.613][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:07.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:07.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.617][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:07.618][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:07.619][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.619][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:07.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:07.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.623][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:07.624][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:07.625][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.625][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.626][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:07.627][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:07.628][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.628][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.629][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:07.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:07.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.632][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:07.633][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:07.634][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.634][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:07.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:07.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.638][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:07.639][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:07.640][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.640][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:07.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:07.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.644][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:07.645][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:07.645][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.646][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.647][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:07.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:07.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.650][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:07.651][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:07.651][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.652][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.659][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:07.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:07.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:07.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:07.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:07.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:07.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:07.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:07.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:07.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:07.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:07.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:07.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:07.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:07.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:07.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:07.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:07.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:07.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:07.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:07.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:07.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:07.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:07.697][self$createEntryFromContent] Accession numbers: 32151. biodb.TRACE[2024-06-29 16:04:07.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:07.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:07.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:07.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:07.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:07.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:07.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:07.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:07.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:07.706][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:07.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:07.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:07.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:07.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:07.713][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:07.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:07.715][private$loadEntries] Creating entries from ids [1]: "67676". biodb.DEBUG[2024-06-29 16:04:07.716][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:07.717][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67676". biodb.TRACE[2024-06-29 16:04:07.718][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:07.719][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:07.720][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:07.721][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:07.722][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:07.722][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:07.724][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:07.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:07.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:07.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:07.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:07.732][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:07.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:07.733][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67676". biodb.DEBUG[2024-06-29 16:04:07.735][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:07.736][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:07.737][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67676". biodb.TRACE[2024-06-29 16:04:08.087][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67676). biodb.DEBUG[2024-06-29 16:04:08.427][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:08.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f87eff9f669415e5528b4d9281ce70e2.content" biodb.TRACE[2024-06-29 16:04:08.431][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f87eff9f669415e5528b4d9281ce70e2.request" biodb.TRACE[2024-06-29 16:04:08.433][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67676.xml" biodb.DEBUG[2024-06-29 16:04:08.435][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:08.435][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:08.436][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:08.438][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:08.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:08.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:08.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:08.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:08.445][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:08.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:08.447][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:08.448][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:08.449][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.449][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:08.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:08.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.453][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:08.454][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:08.455][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.456][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.457][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:08.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:08.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.460][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:08.461][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:08.462][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.462][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.463][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:08.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:08.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.466][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:08.467][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:08.468][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.469][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:08.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:08.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.473][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:08.473][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:08.474][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.475][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:08.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:08.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.479][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:08.480][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:08.481][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.481][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.482][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:08.483][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:08.484][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.484][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.485][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:08.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:08.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.488][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:08.489][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:08.490][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.490][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:08.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:08.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.494][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:08.495][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:08.496][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.496][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:08.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:08.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.501][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:08.502][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:08.502][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.503][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.504][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:08.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:08.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.507][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:08.508][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:08.508][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.509][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.510][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:08.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:08.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:08.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:08.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:08.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:08.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:08.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:08.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:08.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:08.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:08.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:08.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:08.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:08.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:08.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:08.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:08.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:08.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:08.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:08.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:08.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:08.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:08.544][self$createEntryFromContent] Accession numbers: 67676. biodb.TRACE[2024-06-29 16:04:08.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:08.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:08.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:08.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:08.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:08.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:08.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:08.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:08.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:08.554][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:08.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:08.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:08.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:08.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:08.561][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:08.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:08.563][private$loadEntries] Creating entries from ids [1]: "69690". biodb.DEBUG[2024-06-29 16:04:08.564][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:08.565][cch$loadFileContent] Trying to load 1 files from cache: [1]: "69690". biodb.TRACE[2024-06-29 16:04:08.566][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:08.567][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:08.567][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:08.568][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:08.569][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:08.570][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:08.572][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:08.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:08.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:08.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:08.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:08.579][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:08.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:08.580][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69690". biodb.DEBUG[2024-06-29 16:04:08.582][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:08.583][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:08.584][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69690". biodb.TRACE[2024-06-29 16:04:08.928][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69690). biodb.DEBUG[2024-06-29 16:04:09.278][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:09.280][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ce43467f7e4550d502ff0cc79c06666.content" biodb.TRACE[2024-06-29 16:04:09.283][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ce43467f7e4550d502ff0cc79c06666.request" biodb.TRACE[2024-06-29 16:04:09.285][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/69690.xml" biodb.DEBUG[2024-06-29 16:04:09.286][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:09.287][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:09.288][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:09.289][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:09.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:09.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:09.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:09.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:09.302][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:09.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:09.311][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:09.312][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:09.313][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.314][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:09.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:09.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.318][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:09.319][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:09.320][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.320][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.321][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:09.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:09.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.325][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:09.325][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:09.326][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.327][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:09.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:09.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.331][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:09.332][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:09.332][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.333][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:09.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:09.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.337][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:09.338][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:09.339][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.339][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:09.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:09.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.343][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:09.344][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:09.345][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.346][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.347][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:09.347][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:09.348][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.349][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.350][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:09.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:09.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.353][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:09.354][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:09.354][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.355][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:09.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:09.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.359][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:09.360][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:09.361][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.362][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.363][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:09.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:09.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.366][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:09.366][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:09.367][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.368][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.369][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:09.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:09.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.372][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:09.373][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:09.373][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.374][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.375][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:09.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:09.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:09.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:09.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:09.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:09.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:09.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:09.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:09.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:09.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:09.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:09.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:09.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:09.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:09.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:09.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:09.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:09.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:09.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:09.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:09.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:09.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.409][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:09.409][self$createEntryFromContent] Accession numbers: 69690. biodb.TRACE[2024-06-29 16:04:09.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:09.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:09.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:09.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:09.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:09.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:09.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:09.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:09.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:09.420][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:09.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:09.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:09.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:09.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:09.427][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:09.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:09.429][private$loadEntries] Creating entries from ids [1]: "69734". biodb.DEBUG[2024-06-29 16:04:09.430][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:09.431][cch$loadFileContent] Trying to load 1 files from cache: [1]: "69734". biodb.TRACE[2024-06-29 16:04:09.432][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:09.433][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:09.434][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:09.434][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:09.435][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:09.436][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:09.438][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:09.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:09.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:09.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:09.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:09.446][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:09.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:09.447][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69734". biodb.DEBUG[2024-06-29 16:04:09.449][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:09.450][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:09.451][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69734". biodb.TRACE[2024-06-29 16:04:09.794][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69734). biodb.DEBUG[2024-06-29 16:04:10.160][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:10.162][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3ed7db8dba94801a8856f9bde313afe1.content" biodb.TRACE[2024-06-29 16:04:10.165][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3ed7db8dba94801a8856f9bde313afe1.request" biodb.TRACE[2024-06-29 16:04:10.167][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/69734.xml" biodb.DEBUG[2024-06-29 16:04:10.168][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:10.169][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:10.170][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:10.171][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:10.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:10.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:10.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:10.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:10.178][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:10.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:10.181][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:10.182][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:10.183][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.183][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:10.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:10.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.187][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:10.188][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:10.189][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.190][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.191][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:10.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:10.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.194][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:10.195][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:10.196][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.196][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.197][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:10.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:10.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.200][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:10.201][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:10.202][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.203][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:10.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:10.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.207][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:10.207][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:10.208][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.209][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:10.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:10.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.213][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:10.214][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:10.215][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.215][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.216][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:10.217][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:10.218][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.219][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.220][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:10.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:10.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.223][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:10.224][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:10.224][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.225][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:10.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:10.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.229][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:10.230][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:10.231][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.231][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:10.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:10.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.236][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:10.236][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:10.237][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.238][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.239][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:10.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:10.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.242][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:10.243][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:10.243][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.244][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.245][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:10.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:10.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:10.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:10.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:10.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:10.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:10.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:10.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:10.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:10.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:10.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:10.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:10.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:10.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:10.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:10.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:10.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:10.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:10.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:10.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:10.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:10.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:10.289][self$createEntryFromContent] Accession numbers: 69734. biodb.TRACE[2024-06-29 16:04:10.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:10.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:10.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:10.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:10.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:10.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:10.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:10.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:10.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:10.299][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:10.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:10.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:10.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:10.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:10.306][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:10.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:10.307][private$loadEntries] Creating entries from ids [1]: "79978". biodb.DEBUG[2024-06-29 16:04:10.308][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:10.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "79978". biodb.TRACE[2024-06-29 16:04:10.310][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:10.311][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:10.312][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:10.313][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:10.313][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:10.314][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:10.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:10.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:10.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:10.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:10.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:10.323][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:10.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:10.325][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79978". biodb.DEBUG[2024-06-29 16:04:10.327][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:10.328][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:10.329][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79978". biodb.TRACE[2024-06-29 16:04:10.670][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79978). biodb.DEBUG[2024-06-29 16:04:11.004][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:11.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fb887d003d6fc3b4aa767483d261b31c.content" biodb.TRACE[2024-06-29 16:04:11.008][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fb887d003d6fc3b4aa767483d261b31c.request" biodb.TRACE[2024-06-29 16:04:11.010][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/79978.xml" biodb.DEBUG[2024-06-29 16:04:11.012][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:11.013][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:11.014][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:11.015][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:11.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:11.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:11.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:11.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:11.022][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:11.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:11.025][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.025][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.026][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.027][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.032][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:11.032][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:11.033][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.034][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.035][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:11.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:11.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.038][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:11.038][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:11.039][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.040][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.041][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:11.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:11.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.044][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:11.045][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:11.046][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.047][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:11.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:11.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.050][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:11.051][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:11.052][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.053][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.054][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:11.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:11.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.057][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:11.058][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:11.058][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.059][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.060][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:11.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:11.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.063][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:11.064][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:11.065][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.065][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.066][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:11.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:11.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.070][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.070][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.071][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.072][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.076][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:11.077][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:11.077][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.078][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:11.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:11.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.082][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:11.083][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:11.084][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.085][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.086][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:11.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:11.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.089][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:11.090][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:11.090][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.091][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.092][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:11.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:11.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:11.126][self$createEntryFromContent] Accession numbers: 79978. biodb.TRACE[2024-06-29 16:04:11.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:11.136][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:11.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:11.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:11.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:11.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:11.143][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:11.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:11.144][private$loadEntries] Creating entries from ids [1]: "88771". biodb.DEBUG[2024-06-29 16:04:11.145][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-06-29 16:04:11.146][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88771". biodb.TRACE[2024-06-29 16:04:11.147][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-06-29 16:04:11.148][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-06-29 16:04:11.149][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-06-29 16:04:11.150][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-06-29 16:04:11.151][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-06-29 16:04:11.151][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-06-29 16:04:11.153][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:11.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:11.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:11.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:11.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:11.160][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:11.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:11.162][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88771". biodb.DEBUG[2024-06-29 16:04:11.164][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-06-29 16:04:11.165][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-06-29 16:04:11.166][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88771". biodb.TRACE[2024-06-29 16:04:11.505][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88771). biodb.DEBUG[2024-06-29 16:04:11.840][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-06-29 16:04:11.842][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f96325cdb7f39b42d0ab67a7fc41aced.content" biodb.TRACE[2024-06-29 16:04:11.845][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f96325cdb7f39b42d0ab67a7fc41aced.request" biodb.TRACE[2024-06-29 16:04:11.847][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88771.xml" biodb.DEBUG[2024-06-29 16:04:11.848][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-06-29 16:04:11.849][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-06-29 16:04:11.850][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-06-29 16:04:11.852][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:11.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:11.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:11.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:11.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:11.859][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:11.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:11.861][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.862][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.862][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.863][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.867][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:11.868][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:11.869][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.870][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.870][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:11.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:11.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.874][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:11.874][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:11.875][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.876][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.877][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:11.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:11.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.891][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:11.892][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:11.893][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.894][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:11.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:11.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.898][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:11.899][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:11.900][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.900][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:11.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:11.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.905][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:11.906][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:11.906][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.907][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.908][ef$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:11.909][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:11.909][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.910][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.911][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-06-29 16:04:11.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:11.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.914][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.915][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.915][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.916][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.920][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:11.921][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:11.922][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.922][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.923][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:11.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:11.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.926][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:11.927][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:11.928][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.928][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.929][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-06-29 16:04:11.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:11.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.932][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:11.933][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:11.934][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.934][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.935][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:11.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:11.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:11.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:11.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:11.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:11.969][self$createEntryFromContent] Accession numbers: 88771. biodb.TRACE[2024-06-29 16:04:11.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:11.979][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:11.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:11.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:11.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:11.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:11.986][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:11.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:11.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:11.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:11.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:11.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:11.997][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:11.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:11.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.004][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.015][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:12.016][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.023][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.031][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.031][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.032][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.033][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.034][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.034][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.035][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.036][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.037][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.037][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.038][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.039][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.040][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.040][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.041][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.042][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.043][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.044][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.044][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.045][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.055][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:04:12.056][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.063][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.071][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.072][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.072][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.073][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.074][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.075][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.075][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.076][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.077][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.077][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.078][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.079][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.080][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.080][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.081][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.082][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.083][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.083][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.084][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.085][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.095][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-06-29 16:04:12.096][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.103][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.111][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.111][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.112][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.113][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.114][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.115][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.115][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.116][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.117][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.117][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.118][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.119][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.120][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.120][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.121][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.122][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.123][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.123][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.124][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.125][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.135][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-06-29 16:04:12.135][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:12.136][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:12.138][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.153][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:12.155][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:12.158][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:12.159][cch$loadFileContent] Trying to load 1 files from cache: [1]: "a035d13a630066423fab6713592c5e52". biodb.TRACE[2024-06-29 16:04:12.160][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:12.162][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a035d13a630066423fab6713592c5e52.content". biodb.DEBUG[2024-06-29 16:04:12.166][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.173][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.184][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.191][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.202][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.208][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.219][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.226][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.237][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:12.239][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.246][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.254][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.255][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.256][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.257][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.257][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.258][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.259][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.260][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.260][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.261][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.262][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.263][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.263][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.264][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.265][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.266][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.266][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.267][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.268][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.269][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.279][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-06-29 16:04:12.280][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.287][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.294][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.295][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.296][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.296][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.297][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.298][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.298][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.299][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.300][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.301][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.301][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.302][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.303][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.304][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.304][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.305][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.306][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.306][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.307][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.308][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.318][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-06-29 16:04:12.318][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.325][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.333][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.333][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.334][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.335][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.335][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.336][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.337][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.338][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.338][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.339][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.340][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.341][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.341][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.342][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.343][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.343][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.344][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.345][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.345][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.346][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.356][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-06-29 16:04:12.357][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:12.358][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:12.375][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.382][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:12.384][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:12.387][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:12.388][cch$loadFileContent] Trying to load 1 files from cache: [1]: "a035d13a630066423fab6713592c5e52". biodb.TRACE[2024-06-29 16:04:12.389][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:12.390][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a035d13a630066423fab6713592c5e52.content". biodb.DEBUG[2024-06-29 16:04:12.394][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.408][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.419][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.426][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.436][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.443][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.453][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.459][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.470][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.477][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.487][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.494][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.504][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.511][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.521][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:12.523][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.529][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.537][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.537][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.538][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.539][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.539][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.540][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.541][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.542][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.542][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.543][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.544][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.545][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.545][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.546][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.547][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.547][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.548][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.549][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.549][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.550][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.560][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-06-29 16:04:12.560][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.568][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.575][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.576][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.576][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.577][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.578][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.579][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.579][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.580][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.581][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.581][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.582][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.583][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.584][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.585][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.585][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.586][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.587][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.588][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.588][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.589][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.599][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-06-29 16:04:12.599][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.607][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.615][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.615][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.616][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.617][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.618][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.618][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.619][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.620][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.620][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.621][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.622][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.623][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.624][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.624][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.625][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.626][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.626][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.627][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.628][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.629][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.638][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [34764]. biodb.DEBUG[2024-06-29 16:04:12.639][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:12.640][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:12.641][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.648][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:12.651][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:12.660][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:12.661][cch$loadFileContent] Trying to load 1 files from cache: [1]: "365d4ea5e0e90826806fec708da6c9ab". biodb.TRACE[2024-06-29 16:04:12.662][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:12.663][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/365d4ea5e0e90826806fec708da6c9ab.content". biodb.DEBUG[2024-06-29 16:04:12.669][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.676][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.686][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.693][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.703][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.710][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.720][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.727][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.737][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:12.739][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.746][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.753][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.754][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.754][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.755][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.756][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.757][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.757][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.758][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.759][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.759][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.760][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.761][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.762][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.762][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.763][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.764][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.765][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.765][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.766][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.767][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.776][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [2535]. biodb.DEBUG[2024-06-29 16:04:12.777][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.784][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.792][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.793][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.793][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.794][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.795][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.796][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.796][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.797][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.798][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.799][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.799][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.800][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.801][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.801][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.802][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.803][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.804][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.805][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.805][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.806][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.816][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:04:12.817][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.824][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.831][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.832][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.832][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.833][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.834][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.835][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.835][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.836][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.837][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.838][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.838][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.839][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.840][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.841][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.841][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.842][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.843][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.843][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.844][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.845][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.855][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-06-29 16:04:12.855][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:12.856][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:12.858][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.865][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:12.867][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=409.9*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:12.870][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:12.871][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7b0416ab2d5cbf869f248000c039a8e8". biodb.TRACE[2024-06-29 16:04:12.872][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:12.873][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7b0416ab2d5cbf869f248000c039a8e8.content". biodb.DEBUG[2024-06-29 16:04:12.874][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.881][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.892][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.899][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.917][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.924][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.934][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.941][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.951][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.958][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:12.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:12.968][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:12.969][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:12.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:12.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:12.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:12.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:12.976][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:12.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:12.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.984][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.984][private$selectFields] biodb.TRACE[2024-06-29 16:04:12.985][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:12.986][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:12.986][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.987][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.988][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.989][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.989][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.990][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.991][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.991][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.992][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.993][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.993][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:12.994][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.995][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.996][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:12.996][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:12.997][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:12.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:12.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.007][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [31303]. biodb.DEBUG[2024-06-29 16:04:13.008][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.015][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.022][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.023][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.023][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.024][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.025][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.025][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.026][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.027][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.028][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.028][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.029][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.030][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.030][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.031][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.032][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.033][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.034][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.034][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.035][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.036][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.046][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [81767]. biodb.DEBUG[2024-06-29 16:04:13.046][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.053][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.062][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.062][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.063][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.064][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.064][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.065][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.066][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.066][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.067][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.068][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.069][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.070][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.070][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.071][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.072][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.072][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.073][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.074][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.075][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.076][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.086][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [131378]. biodb.DEBUG[2024-06-29 16:04:13.086][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:13.087][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:13.105][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.112][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:13.115][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:13.117][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:13.118][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-06-29 16:04:13.119][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:13.120][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-06-29 16:04:13.123][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:13.125][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:13.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-06-29 16:04:13.127][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:13.128][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-06-29 16:04:13.130][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.137][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.148][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.155][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.172][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.180][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.191][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:13.193][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.200][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.207][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.208][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.209][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.209][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.210][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.211][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.212][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.213][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.213][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.214][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.215][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.216][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.216][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.217][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.218][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.218][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.219][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.220][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.221][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.221][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.231][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-06-29 16:04:13.232][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.240][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.247][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.248][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.249][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.250][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.250][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.251][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.252][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.252][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.253][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.254][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.255][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.255][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.256][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.257][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.258][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.259][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.259][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.260][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.261][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.261][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.272][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:04:13.273][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.280][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.287][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.288][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.289][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.289][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.290][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.291][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.291][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.292][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.293][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.294][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.294][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.295][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.296][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.296][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.297][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.298][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.299][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.299][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.300][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.301][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.311][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-06-29 16:04:13.312][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:13.313][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:13.314][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.321][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:13.323][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:13.326][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:13.327][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7269bbea581f1e243800f8ee4e0f4fdb". biodb.TRACE[2024-06-29 16:04:13.328][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:13.329][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content". biodb.DEBUG[2024-06-29 16:04:13.331][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.338][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.349][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.357][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.368][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.375][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.386][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:13.388][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.395][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.403][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.404][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.404][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.405][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.406][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.406][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.407][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.408][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.409][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.409][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.410][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.411][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.412][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.412][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.413][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.414][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.415][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.415][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.416][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.417][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.433][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:04:13.434][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.441][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.448][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.449][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.450][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.450][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.451][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.452][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.452][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.453][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.454][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.454][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.455][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.456][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.457][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.457][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.458][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.459][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.459][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.460][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.461][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.461][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.471][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-06-29 16:04:13.472][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.479][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.486][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.487][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.488][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.488][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.489][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.490][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.490][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.491][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.492][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.492][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.493][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.494][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.495][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.495][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.496][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.497][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.498][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.498][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.499][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.500][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.509][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-06-29 16:04:13.510][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:13.511][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:13.512][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.520][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:13.522][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:13.524][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:13.525][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-06-29 16:04:13.526][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:13.527][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-06-29 16:04:13.530][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.536][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.547][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.554][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.564][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.570][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.580][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:13.582][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.589][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.596][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.597][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.597][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.598][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.599][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.600][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.600][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.601][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.602][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.602][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.603][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.604][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.605][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.605][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.606][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.607][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.607][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.608][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.609][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.610][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.620][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-06-29 16:04:13.620][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.628][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.635][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.636][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.637][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.637][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.638][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.639][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.640][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.641][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.641][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.642][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.643][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.644][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.644][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.645][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.646][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.647][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.648][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.648][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.649][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.650][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.660][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [64199]. biodb.DEBUG[2024-06-29 16:04:13.660][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.668][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.682][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.683][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.684][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.685][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.685][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.686][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.687][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.688][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.689][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.690][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.690][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.691][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.692][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.693][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.694][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.695][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.695][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.696][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.697][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.698][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.708][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65648]. biodb.DEBUG[2024-06-29 16:04:13.708][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:13.709][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:13.727][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.734][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:13.737][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:13.739][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:13.740][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26eec570aadd234892b573eb0777bd78". biodb.TRACE[2024-06-29 16:04:13.741][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:13.742][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26eec570aadd234892b573eb0777bd78.content". biodb.DEBUG[2024-06-29 16:04:13.744][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.751][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.758][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.762][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.769][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.780][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.786][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.798][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.805][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.816][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.823][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.834][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.841][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.851][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.859][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.869][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.877][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:13.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:13.887][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:13.889][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.896][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.904][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.905][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.905][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.906][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.907][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.907][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.908][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.909][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.910][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.910][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.911][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.912][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.913][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.913][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.914][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.915][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.916][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.917][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.917][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.918][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.928][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-06-29 16:04:13.929][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.936][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.951][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.952][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.953][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.953][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.954][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.955][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.956][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.957][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.957][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.958][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.959][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.959][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.960][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.961][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.962][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.963][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.964][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.964][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.965][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.966][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:13.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.976][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-06-29 16:04:13.977][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:13.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:13.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:13.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:13.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:13.984][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:13.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:13.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.992][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.992][private$selectFields] biodb.TRACE[2024-06-29 16:04:13.993][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:13.994][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:13.994][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:13.995][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.996][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.997][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:13.997][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:13.998][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.999][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:13.999][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.000][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.001][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.002][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.002][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.003][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.004][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.005][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.005][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:14.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.015][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-06-29 16:04:14.016][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:14.017][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:14.019][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.026][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:14.028][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.2*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:14.031][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:14.032][cch$loadFileContent] Trying to load 1 files from cache: [1]: "20c224089a82bbffabd2e7dbc67cfae3". biodb.TRACE[2024-06-29 16:04:14.033][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:14.034][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/20c224089a82bbffabd2e7dbc67cfae3.content". biodb.DEBUG[2024-06-29 16:04:14.039][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.046][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.057][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.064][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.075][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.082][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.092][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.099][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.110][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.117][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.128][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.135][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.146][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.153][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.164][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.171][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.182][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.188][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.206][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.213][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.225][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.231][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.242][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.249][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.259][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.266][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.277][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.285][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.296][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.302][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.313][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.321][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.332][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.338][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.349][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.356][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.367][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.375][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.385][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.392][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.403][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.410][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.421][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.428][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.439][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.446][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.457][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.470][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.475][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.482][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.490][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.500][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.507][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.517][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.524][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.535][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.543][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.554][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.561][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.572][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.580][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.591][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:14.592][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.599][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.607][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.608][private$selectFields] biodb.TRACE[2024-06-29 16:04:14.609][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:14.609][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:14.610][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.611][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.612][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.612][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.613][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.614][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.615][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.615][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.616][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.617][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.617][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.618][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.619][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.620][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.621][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.621][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:14.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.631][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-06-29 16:04:14.632][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.640][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.647][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.648][private$selectFields] biodb.TRACE[2024-06-29 16:04:14.649][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:14.649][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:14.650][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.651][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.652][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.653][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.653][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.654][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.655][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.655][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.656][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.657][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.658][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.658][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.659][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.660][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.661][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.661][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:14.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.672][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-06-29 16:04:14.673][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.680][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.688][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.689][private$selectFields] biodb.TRACE[2024-06-29 16:04:14.689][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:14.690][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:14.691][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.692][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.693][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.693][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.694][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.695][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.696][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.696][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.697][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.698][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.699][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.699][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.700][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.701][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.702][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.703][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:14.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.713][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-06-29 16:04:14.714][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:14.715][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:14.716][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.723][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:14.732][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:14.735][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:14.736][cch$loadFileContent] Trying to load 1 files from cache: [1]: "a035d13a630066423fab6713592c5e52". biodb.TRACE[2024-06-29 16:04:14.737][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:14.739][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a035d13a630066423fab6713592c5e52.content". biodb.DEBUG[2024-06-29 16:04:14.743][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.751][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.758][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.762][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.769][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.780][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.788][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.799][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.806][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:14.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:14.817][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:14.819][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.826][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.833][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.834][private$selectFields] biodb.TRACE[2024-06-29 16:04:14.835][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:14.836][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:14.836][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.837][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.838][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.839][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.839][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.840][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.841][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.842][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.843][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.843][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.844][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.845][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.846][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.846][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.847][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.848][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:14.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.859][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-06-29 16:04:14.860][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.867][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.875][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.876][private$selectFields] biodb.TRACE[2024-06-29 16:04:14.876][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:14.877][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:14.878][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.879][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.880][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.880][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.885][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.886][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.887][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.888][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.889][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.889][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.890][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.891][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.892][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.892][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.893][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.894][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:14.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.905][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-06-29 16:04:14.906][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:14.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:14.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:14.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:14.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:14.913][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:14.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:14.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.921][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.922][private$selectFields] biodb.TRACE[2024-06-29 16:04:14.923][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:14.924][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:14.925][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.925][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.926][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.927][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.928][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.929][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.929][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.930][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.931][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.932][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.933][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-06-29 16:04:14.933][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.934][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.935][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.936][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.937][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-06-29 16:04:14.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:14.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.947][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-06-29 16:04:14.948][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:14.949][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-06-29 16:04:14.966][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:04:14.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:04:14.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.969][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:04:14.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:04:14.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.973][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:04:14.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:04:14.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-29 16:04:14.979][biodb::testThat] biodb.INFO [2024-06-29 16:04:14.980][biodb::testThat] Running test function test_annotateMzValues_additional_fields (" Additional fields are accepted in annotateMzValues() "). biodb.INFO [2024-06-29 16:04:14.981][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-29 16:04:14.982][biodb::testThat] biodb.TRACE[2024-06-29 16:04:14.984][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:04:14.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:04:14.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.987][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:04:14.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:04:14.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.990][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-29 16:04:14.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-29 16:04:14.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:14.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:14.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:14.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:14.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:14.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:14.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:15.039][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:15.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:15.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:15.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:15.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:15.046][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:15.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:15.049][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:15.052][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:15.053][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-06-29 16:04:15.053][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:15.054][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-06-29 16:04:15.056][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:15.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:15.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:15.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:15.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:15.064][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:15.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:15.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:15.075][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:15.078][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:15.079][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-06-29 16:04:15.080][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:15.081][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-06-29 16:04:15.083][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:15.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:15.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:15.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:15.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:15.090][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:15.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:15.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:15.101][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:15.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:15.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:15.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:15.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:15.109][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:15.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:15.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:15.120][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:15.121][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:15.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:15.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:15.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:15.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:15.128][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:15.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:15.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.135][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.139][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.148][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.151][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.161][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.167][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.170][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.185][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.188][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.197][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.200][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.203][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:15.203][private$selectFields] biodb.TRACE[2024-06-29 16:04:15.204][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:15.205][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:15.206][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:15.206][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.207][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.208][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.209][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.209][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.210][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.211][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.212][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.212][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.213][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.214][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.215][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.215][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.216][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.217][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.218][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.218][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.219][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.220][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.221][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.221][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.222][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.223][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.224][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.225][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.225][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.226][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.227][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.228][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.229][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.229][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.230][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.231][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.232][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.232][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.233][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.234][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.235][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.235][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.236][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.237][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.238][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.238][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.239][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.240][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.241][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.241][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.242][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.243][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.244][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.245][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.245][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.246][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.247][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.248][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.248][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.249][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.250][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.250][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.251][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.252][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.253][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.254][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.254][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.255][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.256][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.263][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.264][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.265][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.266][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.267][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.268][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.269][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.270][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.270][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.271][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.272][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.273][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.274][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.274][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.275][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.276][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.276][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.277][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.278][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.279][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.280][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.280][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.281][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.282][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.282][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.283][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.284][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.284][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.285][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.286][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.286][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:15.287][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:15.288][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.289][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.289][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.290][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.291][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.292][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.293][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.293][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.294][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.295][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.295][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.296][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.297][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.298][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.298][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.299][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.300][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.301][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.301][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.302][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.303][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.303][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.304][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.305][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.305][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.306][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.307][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.308][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.309][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.309][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.310][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.311][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.311][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.312][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.313][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.313][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.314][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.315][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.316][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.317][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.317][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.318][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.319][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.319][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.321][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:15.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.330][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.334][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.337][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.349][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.352][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.355][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.395][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.398][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.401][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.416][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.419][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.427][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [192288, 0, 192288, C27H54O2, InChI=1S/C27H54O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27(28)29-2/h3-26H2,1-2H3, ...]. biodb.DEBUG[2024-06-29 16:04:15.428][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:15.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:15.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:15.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:15.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:15.435][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:15.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:15.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.443][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.446][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.454][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.457][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.460][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.472][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.475][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.490][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.493][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.660][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.663][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.666][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:15.666][private$selectFields] biodb.TRACE[2024-06-29 16:04:15.667][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:15.668][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:15.668][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:15.669][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.670][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.670][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.671][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.672][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.672][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.673][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.674][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.674][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.675][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.676][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.676][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.677][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.678][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.678][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.679][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.680][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.681][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.682][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.682][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.683][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.684][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.684][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.685][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.686][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.686][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.687][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.688][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.688][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.689][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.690][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.690][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.691][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.692][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.693][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.693][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.694][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.695][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.695][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.696][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.697][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.697][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.698][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.699][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.700][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.700][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.701][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.702][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.702][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.703][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.704][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.705][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.705][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.706][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.707][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.707][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.708][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.709][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.709][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.710][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.711][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.711][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.712][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.713][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.713][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.714][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.715][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.715][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.716][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.717][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.717][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.718][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.719][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.719][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.720][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.721][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.721][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.722][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.723][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.723][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.724][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.725][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.726][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.727][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.727][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.728][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.729][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.730][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.731][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.731][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.732][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.733][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.734][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.734][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.735][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.736][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.736][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:15.737][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:15.738][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.738][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.739][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.740][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.741][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.741][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.742][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.743][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.743][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.744][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.745][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.745][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.746][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.747][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.747][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.748][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.749][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.750][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.750][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.751][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.752][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.752][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.753][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.754][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.754][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.755][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.756][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.756][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.757][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.758][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.759][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.759][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.760][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.761][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.761][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.762][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.763][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.763][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.764][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.765][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.766][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.766][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.767][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.768][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.768][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.769][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.770][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.770][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.771][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:15.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.781][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.784][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.787][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.799][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.802][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.805][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.827][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.829][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.833][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.854][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.857][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.860][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.870][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.872][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.876][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.879][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.887][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [15440, 0, 15440, C30H50, InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3/b27-17+,28-18+,29-23+,30-24+, ...]. biodb.DEBUG[2024-06-29 16:04:15.887][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:15.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:15.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:15.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:15.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:15.895][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:15.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:15.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.906][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.909][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.918][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.926][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.932][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.935][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.938][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.953][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.956][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:15.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:15.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:15.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:15.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.964][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.967][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:15.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:15.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.970][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:15.971][private$selectFields] biodb.TRACE[2024-06-29 16:04:15.971][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:15.972][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:15.973][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:15.974][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:15.974][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:15.975][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.976][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.976][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:15.977][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:15.978][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.978][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.979][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.980][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:15.980][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.981][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.982][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:15.983][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:15.983][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.984][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.984][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:15.985][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:15.986][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.987][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.987][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:15.988][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:15.989][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.989][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.990][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.991][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:15.992][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.992][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.993][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.994][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:15.994][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.995][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.996][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.997][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:15.997][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:15.998][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:15.999][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.000][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.000][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.001][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.002][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.002][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.003][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.004][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.004][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.005][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.006][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.006][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.007][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.008][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.009][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.009][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.010][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.011][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.012][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.012][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.013][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.014][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.014][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.015][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.016][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.016][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.017][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.018][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.019][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.019][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.020][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.021][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.021][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.022][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.023][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.024][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.025][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.025][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.026][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.027][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.028][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.028][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.029][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.030][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.030][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.031][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.032][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.033][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.033][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.034][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.035][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.036][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.036][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.037][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.038][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.038][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.039][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.040][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.041][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.041][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.042][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:16.043][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:16.043][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.044][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.045][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.046][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.046][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.047][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.048][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.049][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.049][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.050][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.051][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.051][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.052][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.053][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.053][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.054][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.055][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.056][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.056][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.057][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.058][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.059][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.059][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.060][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.061][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.061][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.062][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.063][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.063][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.064][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.065][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.066][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.066][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.067][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.068][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.069][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.069][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.070][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.071][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.071][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.072][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.073][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.073][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.074][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.075][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:16.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.085][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.088][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.090][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.105][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.108][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.151][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.154][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.157][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.169][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.171][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.174][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.180][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [209892, 0, 209892, C30H50, InChI=1S/C30H50/c1-21(2)11-9-12-22(3)23-15-19-30(8)25-13-14-26-27(4,5)17-10-18-28(26,6)24(25)16-20-29(23,30)7/h11,13,22-24,26H,9-10,12,14-20H2,1-8H3/t22-,23+,24+,26+,28-,29+,30-/m1/s1, ...]. biodb.DEBUG[2024-06-29 16:04:16.181][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:16.182][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:16.184][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:16.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:16.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:16.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:16.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:16.191][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:16.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:16.194][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:16.196][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:16.197][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-06-29 16:04:16.198][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:16.199][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-06-29 16:04:16.201][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:16.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:16.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:16.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:16.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:16.207][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:16.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:16.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:16.218][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:16.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:16.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:16.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:16.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:16.224][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:16.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:16.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:16.235][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:16.237][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:16.239][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-06-29 16:04:16.240][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:16.240][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-06-29 16:04:16.242][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:16.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:16.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:16.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:16.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:16.249][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:16.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:16.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:16.260][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:16.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:16.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:16.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:16.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:16.267][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:16.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:16.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:16.278][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:16.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:16.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:16.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:16.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:16.284][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:16.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:16.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:16.296][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:16.297][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:16.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:16.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:16.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:16.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:16.304][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:16.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:16.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.312][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.315][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.324][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.327][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.341][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.344][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.359][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.362][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.365][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.371][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.374][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.377][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:16.377][private$selectFields] biodb.TRACE[2024-06-29 16:04:16.378][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:16.379][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:16.379][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:16.380][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.381][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.382][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.383][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.383][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.384][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.385][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.385][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.386][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.387][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.388][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.388][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.389][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.390][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.391][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.391][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.392][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.393][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.394][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.395][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.395][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.396][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.401][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.402][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.403][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.404][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.404][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.405][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.406][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.407][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.407][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.408][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.409][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.409][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.410][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.411][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.412][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.412][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.413][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.414][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.414][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.415][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.416][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.416][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.417][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.418][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.418][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.419][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.420][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.421][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.422][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.422][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.423][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.424][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.425][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.425][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.426][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.427][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.428][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.428][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.429][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.430][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.430][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.431][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.432][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.432][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.433][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.434][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.434][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.435][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.436][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.437][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.437][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.438][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.439][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.440][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.440][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.441][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.442][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.443][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.443][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.444][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.445][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.446][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.446][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.447][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.448][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.449][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.449][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.450][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.451][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.452][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.452][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.453][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.454][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.455][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.455][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:16.456][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:16.457][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.458][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.459][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.459][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.460][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.461][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.462][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.462][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.463][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.464][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.464][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.465][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.466][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.467][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.467][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.468][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.469][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.470][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.471][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.471][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.472][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.473][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.473][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.474][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.475][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.476][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.476][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.477][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.478][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.479][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.479][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.480][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.481][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.481][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.482][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.483][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.483][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.484][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.485][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.486][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.486][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.487][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.488][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.488][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.489][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.490][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.491][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.492][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.492][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:16.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.503][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.506][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.509][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.521][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.524][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.549][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.552][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.555][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.577][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.580][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.583][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.595][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.598][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.601][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.608][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4781, 0, 4781, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24+,25-/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:16.609][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:16.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:16.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:16.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:16.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:16.616][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:16.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:16.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.624][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.627][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.637][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.639][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.655][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.658][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.661][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.676][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.679][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.685][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.688][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.691][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.694][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:16.695][private$selectFields] biodb.TRACE[2024-06-29 16:04:16.695][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:16.696][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:16.697][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:16.698][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.698][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.699][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.700][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.700][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.701][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.702][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.702][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.703][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.704][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.705][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.705][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.706][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.707][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.707][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.708][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.709][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.709][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.710][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.711][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.712][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.712][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.713][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.714][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.714][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.715][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.716][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.717][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.717][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.718][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.719][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.720][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.720][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.721][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.722][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.723][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.723][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.724][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.725][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.725][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.726][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.727][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.727][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.728][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.729][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.730][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.730][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.731][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.732][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.732][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.733][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.734][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.735][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.735][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.736][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.737][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.738][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.739][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.739][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.740][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.741][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.742][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.742][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.743][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.744][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.745][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.745][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.746][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.747][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.747][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.748][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.749][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.750][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.750][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.751][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.752][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.752][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.753][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.754][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.755][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.755][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.756][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.757][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.758][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.758][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.759][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.760][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.761][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.761][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.762][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.763][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.764][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.765][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.765][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.766][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.767][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.767][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:16.768][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:16.769][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.770][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.770][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.771][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.772][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.773][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.774][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.774][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.775][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.776][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.777][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.778][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.778][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.779][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.780][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.781][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.781][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.782][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.783][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.784][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.785][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.785][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.786][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.787][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.788][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.788][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.789][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.790][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.791][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.791][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.792][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.793][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.794][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.794][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.795][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.796][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.797][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.797][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.798][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.799][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.800][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.800][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.801][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.802][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.803][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.803][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.804][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.805][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.805][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:16.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.815][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.819][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.822][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.834][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.837][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.840][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.849][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.852][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.855][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.861][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.864][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.867][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.889][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.892][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.895][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.911][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.914][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.917][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.924][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [16587, 0, 16587, C27H44O7, InChI=1S/C27H44O7/c1-23(2,32)9-8-22(31)26(5,33)21-7-11-27(34)16-12-18(28)17-13-19(29)20(30)14-24(17,3)15(16)6-10-25(21,27)4/h12,15,17,19-22,29-34H,6-11,13-14H2,1-5H3/t15-,17-,19+,20-,21-,22+,24+,25+,26+,27+/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:16.925][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:16.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:16.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:16.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:16.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:16.932][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:16.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:16.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:16.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:16.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.939][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.942][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:16.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:16.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:16.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.951][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.954][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:16.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:16.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:16.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:16.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.963][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:16.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:16.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.968][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.971][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:16.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:16.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:16.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.986][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.989][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:16.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:16.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.995][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:16.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:16.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:16.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:16.998][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:16.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:16.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.000][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.003][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:17.004][private$selectFields] biodb.TRACE[2024-06-29 16:04:17.005][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:17.005][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:17.006][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:17.007][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.008][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.008][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.009][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.010][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.010][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.011][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.012][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.013][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.013][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.014][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.015][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.016][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.016][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.017][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.018][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.018][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.019][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.020][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.021][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.021][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.022][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.023][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.024][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.024][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.025][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.026][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.027][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.027][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.028][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.029][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.029][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.030][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.031][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.032][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.032][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.033][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.034][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.035][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.035][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.036][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.037][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.037][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.038][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.039][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.040][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.040][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.041][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.042][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.043][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.043][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.044][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.045][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.046][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.047][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.047][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.048][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.049][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.049][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.050][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.051][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.052][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.052][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.053][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.054][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.055][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.055][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.056][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.057][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.058][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.058][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.059][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.060][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.061][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.061][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.062][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.063][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.064][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.064][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.065][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.066][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.067][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.067][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.068][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.069][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.069][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.070][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.071][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.071][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.072][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.073][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.074][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.074][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.075][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.076][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.076][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.077][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:17.078][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:17.079][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.080][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.080][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.081][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.082][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.083][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.083][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.084][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.085][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.086][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.086][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.087][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.088][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.088][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.089][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.090][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.091][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.091][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.092][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.093][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.094][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.094][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.095][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.096][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.097][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.098][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.098][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.099][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.100][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.101][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.101][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.102][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.103][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.104][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.105][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.105][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.106][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.107][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.108][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.108][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.109][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.110][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.111][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.111][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.112][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:17.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.123][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.126][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.129][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.141][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.144][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.151][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.160][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.190][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.193][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.196][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.208][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.211][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.213][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.214][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.220][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [19804, 0, 19804, C27H44O7, InChI=1S/C27H44O7/c1-23(2,32)8-5-9-26(33,15-28)22-7-11-27(34)17-12-19(29)18-13-20(30)21(31)14-24(18,3)16(17)6-10-25(22,27)4/h12,16,18,20-22,28,30-34H,5-11,13-15H2,1-4H3/t16-,18-,20+,21-,22-,24+,25+,26+,27+/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:17.221][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:17.222][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:17.224][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.231][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:17.233][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:17.236][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:17.237][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26d0872875c47c33e8205aa7124e0486". biodb.TRACE[2024-06-29 16:04:17.238][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:17.239][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content". biodb.DEBUG[2024-06-29 16:04:17.240][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.247][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:17.257][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.264][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:17.275][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.282][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:17.293][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.300][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:17.311][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.318][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:17.329][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.336][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:17.348][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.355][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:17.365][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.372][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:17.383][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:17.386][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:17.386][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-06-29 16:04:17.387][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:17.388][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-06-29 16:04:17.390][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.397][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:17.412][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.419][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:17.429][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.436][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:17.446][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:17.448][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.454][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.462][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.465][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.474][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.477][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.491][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.494][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.508][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.511][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.520][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.523][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.526][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:17.526][private$selectFields] biodb.TRACE[2024-06-29 16:04:17.527][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:17.528][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:17.529][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:17.529][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.530][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.531][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.531][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.532][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.533][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.534][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.534][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.535][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.536][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.537][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.537][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.538][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.539][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.539][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.540][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.541][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.541][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.542][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.543][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.544][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.544][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.545][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.546][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.546][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.547][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.548][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.549][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.549][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.550][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.551][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.551][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.552][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.553][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.553][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.554][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.555][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.556][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.557][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.557][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.558][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.559][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.560][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.560][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.561][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.562][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.562][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.563][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.564][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.565][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.565][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.566][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.567][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.568][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.568][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.569][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.570][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.570][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.571][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.572][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.572][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.573][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.574][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.575][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.575][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.576][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.577][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.578][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.578][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.579][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.580][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.580][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.581][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.582][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.583][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.583][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.584][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.585][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.586][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.586][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.587][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.588][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.589][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.589][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.590][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.591][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.591][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.592][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.593][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.594][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.594][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.595][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.596][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.597][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.597][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.598][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.599][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:17.599][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:17.600][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.601][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.620][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.621][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.622][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.623][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.623][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.624][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.625][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.625][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.626][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.627][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.627][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.628][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.629][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.630][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.630][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.631][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.632][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.633][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.633][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.634][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.635][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.636][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.636][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.637][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.638][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.639][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.639][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.640][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.641][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.642][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.643][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.643][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.644][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.645][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.645][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.646][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.647][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.648][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.648][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.649][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.650][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.651][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.652][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.652][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.653][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.654][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.655][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:17.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.665][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.668][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.671][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.686][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.689][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.692][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.701][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.707][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.713][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.716][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.718][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.719][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.741][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.744][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.747][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.758][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.759][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.762][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.765][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.772][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [7799, 0, 7799, C16H31N2O8P, InChI=1S/C16H28N2O4.H3O4P/c1-5-12(6-2)22-14-9-11(16(20)21-7-3)8-13(17)15(14)18-10(4)19;1-5(2,3)4/h9,12-15H,5-8,17H2,1-4H3,(H,18,19);(H3,1,2,3,4)/t13-,14+,15+;/m0./s1, ...]. biodb.DEBUG[2024-06-29 16:04:17.773][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:17.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:17.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:17.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:17.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:17.781][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:17.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:17.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.788][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.791][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.800][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.803][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.813][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.819][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.822][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.837][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.840][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.843][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.849][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.852][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.855][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:17.856][private$selectFields] biodb.TRACE[2024-06-29 16:04:17.856][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:17.857][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:17.858][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:17.859][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.860][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.860][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.861][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.862][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.863][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.864][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.864][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.865][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.866][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.866][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.867][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.868][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.868][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.869][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.870][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.871][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.871][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.872][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.873][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.873][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.874][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.875][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.875][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.876][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.877][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.878][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.879][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.879][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.880][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.881][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.882][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.882][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.883][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.884][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.885][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.886][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.886][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.887][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.888][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.888][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.889][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.890][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.891][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.892][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.892][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.893][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.894][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.894][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.895][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.896][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.897][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.897][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.898][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.899][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.899][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.900][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.901][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.902][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.902][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.903][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.904][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.904][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.905][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.906][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.906][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.907][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.908][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.908][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.909][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.910][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.911][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.911][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.912][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:17.913][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.913][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.914][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.915][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.915][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.916][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.917][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.918][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.918][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.919][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.920][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.920][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.921][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.922][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.927][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.928][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.928][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.929][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.930][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.930][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.931][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.932][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.932][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:17.933][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:17.934][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.934][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.935][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.936][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.936][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.937][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.938][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.938][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.939][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.940][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.941][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.941][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.942][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.943][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.943][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.944][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.944][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:17.945][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:17.946][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.947][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.947][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:17.948][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:17.949][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.949][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.950][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.951][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:17.951][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.952][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.952][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.953][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:17.954][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.955][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.955][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:17.956][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:17.957][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.957][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.958][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:17.959][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:17.960][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.960][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.961][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:17.962][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:17.963][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.964][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.964][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:17.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:17.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:17.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.975][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.978][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.981][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:17.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:17.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:17.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.993][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.996][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:17.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:17.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:17.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:17.999][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.002][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.037][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.040][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.043][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.055][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.057][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.060][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.067][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [71954, 0, 71954, C18H21F3N6O2, InChI=1S/C18H21F3N6O2/c19-18(20,21)13-9-15(22)23-11-12(13)14-10-16(26-1-5-28-6-2-26)25-17(24-14)27-3-7-29-8-4-27/h9-11H,1-8H2,(H2,22,23), ...]. biodb.DEBUG[2024-06-29 16:04:18.068][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:18.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:18.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:18.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:18.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:18.075][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:18.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:18.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.082][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.085][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.094][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.097][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.100][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.103][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.109][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.111][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.114][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.129][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.132][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.135][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.141][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.144][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.147][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:18.148][private$selectFields] biodb.TRACE[2024-06-29 16:04:18.148][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:18.149][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:18.150][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:18.151][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.152][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.152][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.153][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.154][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.155][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.155][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.156][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.157][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.158][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.158][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.159][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.160][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.161][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.162][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.162][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.163][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.164][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.165][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.165][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.166][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.171][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.171][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.172][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.173][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.174][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.174][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.175][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.176][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.177][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.177][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.178][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.179][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.179][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.180][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.181][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.182][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.182][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.183][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.184][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.184][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.185][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.186][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.187][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.187][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.188][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.189][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.190][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.190][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.191][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.192][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.193][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.193][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.194][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.195][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.195][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.196][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.197][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.198][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.198][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.199][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.200][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.201][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.201][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.202][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.203][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.203][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.204][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.205][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.206][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.206][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.207][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.208][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.209][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.209][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.210][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.211][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.212][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.212][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.213][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.214][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.215][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.215][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.216][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.217][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.217][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.218][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.219][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.219][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.220][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.221][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.222][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.222][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.223][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.224][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.224][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.225][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:18.226][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:18.227][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.227][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.228][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.229][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.229][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.230][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.231][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.231][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.232][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.233][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.233][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.234][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.235][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.236][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.236][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.237][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.238][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.238][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.239][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.240][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.240][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.241][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.242][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.243][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.243][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.244][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.245][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.245][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.246][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.247][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.247][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.248][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.249][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.250][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.250][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.251][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.251][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.252][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.253][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.254][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.254][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.255][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.256][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.257][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.257][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:18.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.267][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.270][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.273][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.287][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.290][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.293][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.296][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.304][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.316][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.329][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.332][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.335][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.348][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.351][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.354][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.360][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [197612, 0, 197612, C18H18O9S, InChI=1S/C18H18O9S/c1-7-3-9(19)13-11(4-7)27-16-8(14(13)21)5-12(28-16)18(25,17(24)26-2)6-10(20)15(22)23/h3-4,10,12,19-20,25H,5-6H2,1-2H3,(H,22,23)/t10-,12+,18?/m1/s1, ...]. biodb.DEBUG[2024-06-29 16:04:18.361][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:18.362][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:18.368][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:18.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:18.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:18.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:18.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:18.375][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:18.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:18.377][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:18.380][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:18.381][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-06-29 16:04:18.382][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:18.383][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-06-29 16:04:18.385][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:18.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:18.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:18.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:18.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:18.392][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:18.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:18.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:18.404][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:18.406][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:18.407][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-06-29 16:04:18.408][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:18.409][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-06-29 16:04:18.410][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:18.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:18.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:18.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:18.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:18.421][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:18.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:18.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:18.432][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:18.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:18.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:18.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:18.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:18.439][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:18.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:18.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:18.449][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:18.451][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:18.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:18.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:18.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:18.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:18.458][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:18.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:18.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.466][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.469][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.500][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.513][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.516][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.520][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.536][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.539][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.548][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.551][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.554][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.558][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.561][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:18.561][private$selectFields] biodb.TRACE[2024-06-29 16:04:18.562][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:18.563][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:18.563][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:18.564][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.565][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.566][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.566][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.567][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.568][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.568][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.569][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.570][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.571][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.572][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.572][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.573][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.574][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.575][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.575][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.576][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.577][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.578][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.579][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.579][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.580][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.581][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.581][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.582][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.583][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.584][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.584][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.585][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.586][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.587][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.587][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.588][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.589][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.590][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.590][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.591][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.592][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.593][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.593][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.594][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.595][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.595][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.596][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.597][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.598][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.599][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.599][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.600][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.601][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.601][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.602][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.603][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.604][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.604][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.605][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.606][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.607][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.607][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.608][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.609][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.610][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.611][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.612][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.612][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.613][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.614][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.615][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.616][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.616][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.617][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.618][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.619][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.619][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.620][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.621][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.622][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.622][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.623][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.624][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.624][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.625][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.626][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.627][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.627][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.628][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.629][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.630][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.630][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.631][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.632][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.633][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.634][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.634][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.635][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.636][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.637][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.637][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.638][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.639][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.639][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.640][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.641][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.642][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.642][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:18.643][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:18.644][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.645][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.645][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.646][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.647][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.648][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.648][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.649][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.650][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.651][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.651][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.652][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.653][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.653][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.654][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.655][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.655][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.656][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.657][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.658][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.658][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.659][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.660][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.660][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.661][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.662][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.663][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.663][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.664][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.665][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.665][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.666][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.667][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.667][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.668][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.669][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.669][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.670][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.671][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.672][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.673][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.673][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.674][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.675][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.676][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:18.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.686][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.693][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.696][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.708][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.714][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.717][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.723][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.752][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.755][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.758][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.764][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.770][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.772][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.775][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.781][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [192288, 0, 192288, C27H54O2, InChI=1S/C27H54O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27(28)29-2/h3-26H2,1-2H3, ...]. biodb.DEBUG[2024-06-29 16:04:18.782][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:18.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:18.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:18.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:18.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:18.789][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:18.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:18.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.796][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.799][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.808][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.811][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.820][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.826][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.829][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.843][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.846][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.855][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.858][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.861][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.864][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.867][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:18.868][private$selectFields] biodb.TRACE[2024-06-29 16:04:18.869][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:18.869][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:18.870][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:18.871][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.871][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.872][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.873][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.873][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.874][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.875][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.876][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.876][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.877][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.878][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.879][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.880][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.880][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.881][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.882][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.883][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.883][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.884][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.885][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.886][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.886][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.887][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.888][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.888][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.889][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.890][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.891][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.891][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.892][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.893][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.893][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.894][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.895][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.895][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.896][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.897][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.898][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.898][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.899][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.900][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.901][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.902][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.902][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.903][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.904][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.905][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.905][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.906][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.907][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.907][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.908][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.909][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.909][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.910][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.911][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.912][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.912][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.913][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.914][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.915][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.915][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.916][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.917][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.918][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.918][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.919][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.920][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.920][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.921][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.922][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.923][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.923][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.924][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.925][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.926][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.926][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.927][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.928][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.928][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.929][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.930][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.930][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.931][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.936][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.937][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.937][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.938][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.939][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.939][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.940][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.941][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.942][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.942][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.943][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.944][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.945][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.945][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.946][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.947][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.947][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.948][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:18.949][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.949][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.950][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:18.951][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:18.952][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.952][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.953][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.954][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.954][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.955][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.956][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.956][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.957][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.958][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:18.959][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.959][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.960][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:18.961][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:18.962][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.962][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.963][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:18.964][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:18.964][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.965][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.966][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:18.966][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:18.967][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.968][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.968][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.969][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:18.970][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.971][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.971][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.972][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:18.973][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.973][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.974][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.975][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:18.975][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.976][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.977][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:18.977][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:18.978][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.979][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.979][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:18.980][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:18.981][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.981][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.982][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:18.983][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:18.984][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.985][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.985][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:18.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:18.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:18.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.995][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:18.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:18.998][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:18.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:18.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.001][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.012][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.015][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.021][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.039][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.042][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.044][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.065][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.068][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.071][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.081][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.084][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.087][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.090][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.097][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [15440, 0, 15440, C30H50, InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3/b27-17+,28-18+,29-23+,30-24+, ...]. biodb.DEBUG[2024-06-29 16:04:19.098][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:19.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:19.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:19.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:19.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:19.105][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:19.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:19.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.113][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.116][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.125][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.128][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.139][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.142][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.145][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.162][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.165][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.175][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.183][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.186][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.189][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.192][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:19.193][private$selectFields] biodb.TRACE[2024-06-29 16:04:19.194][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:19.195][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:19.196][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:19.197][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.198][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.198][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.199][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.200][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.201][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.202][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.203][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.204][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.205][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.205][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.206][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.207][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.208][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.209][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.210][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.211][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.212][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.212][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.213][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.214][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.215][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.216][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.217][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.218][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.219][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.220][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.221][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.221][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.223][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.223][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.224][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.225][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.226][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.227][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.228][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.229][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.230][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.231][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.232][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.233][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.234][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.235][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.236][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.237][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.238][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.239][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.240][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.241][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.243][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.243][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.244][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.245][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.246][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.247][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.248][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.249][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.250][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.251][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.252][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.253][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.254][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.255][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.255][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.256][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.257][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.258][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.259][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.260][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.261][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.262][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.264][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.265][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.266][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.266][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.267][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.268][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.269][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.270][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.271][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.272][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.273][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.274][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.274][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.275][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.276][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.277][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.278][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.279][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.279][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.280][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.281][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.282][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.283][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.284][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.284][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.285][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.286][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.287][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.288][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.288][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.289][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.290][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.291][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.292][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:19.292][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:19.293][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.294][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.295][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.295][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.296][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.297][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.297][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.298][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.299][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.300][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.300][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.301][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.302][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.303][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.303][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.304][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.305][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.306][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.306][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.307][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.308][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.308][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.309][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.310][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.310][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.311][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.312][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.313][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.313][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.314][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.315][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.316][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.316][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.317][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.318][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.319][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.319][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.320][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.321][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.321][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.322][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.323][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.324][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.325][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.325][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:19.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.335][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.339][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.342][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.355][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.358][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.361][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.400][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.403][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.406][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.415][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.418][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.421][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.424][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.430][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [209892, 0, 209892, C30H50, InChI=1S/C30H50/c1-21(2)11-9-12-22(3)23-15-19-30(8)25-13-14-26-27(4,5)17-10-18-28(26,6)24(25)16-20-29(23,30)7/h11,13,22-24,26H,9-10,12,14-20H2,1-8H3/t22-,23+,24+,26+,28-,29+,30-/m1/s1, ...]. biodb.DEBUG[2024-06-29 16:04:19.431][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:19.432][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:19.434][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:19.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:19.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:19.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:19.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:19.441][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:19.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:19.444][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:19.450][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:19.451][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-06-29 16:04:19.451][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:19.452][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-06-29 16:04:19.454][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:19.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:19.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:19.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:19.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:19.461][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:19.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:19.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:19.471][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:19.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:19.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:19.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:19.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:19.477][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:19.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:19.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:19.488][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:19.490][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:19.491][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-06-29 16:04:19.492][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:19.493][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-06-29 16:04:19.495][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:19.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:19.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:19.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:19.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:19.501][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:19.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:19.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:19.511][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:19.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:19.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:19.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:19.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:19.518][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:19.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:19.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:19.528][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:19.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:19.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:19.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:19.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:19.534][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:19.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:19.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:19.545][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:19.546][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:19.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:19.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:19.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:19.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:19.552][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:19.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:19.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.560][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.563][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.571][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.574][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.589][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.592][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.607][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.610][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.621][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.624][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.627][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.630][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:19.631][private$selectFields] biodb.TRACE[2024-06-29 16:04:19.632][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:19.632][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:19.633][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:19.634][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.634][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.635][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.636][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.637][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.637][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.638][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.639][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.639][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.640][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.641][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.641][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.642][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.643][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.643][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.644][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.645][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.646][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.647][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.647][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.648][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.649][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.649][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.650][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.651][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.652][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.653][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.653][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.654][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.655][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.656][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.657][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.657][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.658][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.659][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.659][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.660][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.661][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.662][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.662][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.663][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.664][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.664][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.665][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.666][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.667][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.667][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.668][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.669][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.669][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.670][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.671][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.671][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.672][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.673][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.673][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.674][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.675][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.676][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.676][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.677][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.678][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.678][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.679][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.680][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.681][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.682][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.682][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.683][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.684][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.685][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.685][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.686][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.687][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.687][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.688][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.689][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.690][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.690][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.691][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.696][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.697][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.697][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.698][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.699][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.699][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.700][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.701][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.701][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.702][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.703][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.703][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.704][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.705][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.705][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.706][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.707][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.708][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.708][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.709][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.710][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.711][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.711][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.712][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.713][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:19.713][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:19.714][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.715][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.715][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.716][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.717][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.718][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.718][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.719][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.719][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.720][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.721][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.722][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.722][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.723][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.724][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.724][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.725][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.726][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.726][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.727][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.728][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.728][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.729][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.730][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.730][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.731][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.732][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.732][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.733][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.734][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.735][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.736][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.736][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.737][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.738][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.738][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.739][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.740][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.741][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.741][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.742][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.743][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.743][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.744][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.745][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.746][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.746][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.747][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.748][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:19.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.757][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.760][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.763][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.777][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.780][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.789][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.792][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.801][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.804][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.807][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.827][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.830][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.833][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.845][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.848][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.851][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.858][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4781, 0, 4781, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24+,25-/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:19.859][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:19.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:19.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:19.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:19.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:19.866][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:19.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:19.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.874][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.877][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.886][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.905][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.908][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.923][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.927][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.929][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.932][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.939][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.942][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.945][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.948][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.951][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:19.952][private$selectFields] biodb.TRACE[2024-06-29 16:04:19.952][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:19.953][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:19.954][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:19.954][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.955][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.956][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.956][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.957][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.958][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.958][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.959][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.960][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.961][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.961][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.962][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.962][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:19.963][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:19.964][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.965][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.966][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:19.966][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:19.967][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.968][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.968][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:19.969][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:19.970][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.970][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.971][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.972][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:19.972][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.973][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.974][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.975][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:19.975][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.976][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.977][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.978][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:19.978][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.979][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.980][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:19.981][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:19.981][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.982][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.983][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:19.983][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:19.984][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.985][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.985][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:19.986][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:19.987][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.987][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.988][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.989][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:19.989][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.990][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.991][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:19.992][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:19.993][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.993][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.994][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:19.995][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:19.995][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.996][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.997][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.997][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:19.998][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:19.999][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:19.999][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.000][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.001][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.001][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.002][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.003][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.004][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.004][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.005][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.006][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.007][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.007][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.008][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.009][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.010][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.010][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.011][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.012][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.012][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.013][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.014][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.014][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.015][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.016][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.016][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.017][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.018][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.019][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.020][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.020][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.021][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.022][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.022][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.023][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.024][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.024][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.025][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.026][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.026][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.027][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.028][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:20.029][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:20.029][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.030][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.031][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.032][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.032][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.033][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.034][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.034][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.035][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.036][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.037][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.037][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.038][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.039][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.039][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.040][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.041][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.041][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.042][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.043][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.043][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.044][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.045][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.046][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.047][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.047][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.048][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.049][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.049][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.050][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.051][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.051][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.052][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.053][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.053][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.054][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.055][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.056][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.056][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.057][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.058][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.059][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.059][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.060][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.061][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.062][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.062][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.063][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.064][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:20.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.074][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.077][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.079][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.091][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.094][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.097][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.109][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.115][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.118][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.121][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.124][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.145][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.148][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.150][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.156][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.163][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.166][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.169][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.180][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [16587, 0, 16587, C27H44O7, InChI=1S/C27H44O7/c1-23(2,32)9-8-22(31)26(5,33)21-7-11-27(34)16-12-18(28)17-13-19(29)20(30)14-24(17,3)15(16)6-10-25(21,27)4/h12,15,17,19-22,29-34H,6-11,13-14H2,1-5H3/t15-,17-,19+,20-,21-,22+,24+,25+,26+,27+/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:20.181][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.188][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.195][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.198][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.203][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.206][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.218][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.223][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.226][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.241][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.243][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.255][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.258][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.262][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.264][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.267][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.270][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:20.271][private$selectFields] biodb.TRACE[2024-06-29 16:04:20.271][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:20.272][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:20.273][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:20.273][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.274][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.275][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.275][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.276][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.277][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.277][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.278][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.279][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.279][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.280][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.281][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.282][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.283][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.283][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.284][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.285][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.286][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.286][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.287][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.288][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.288][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.289][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.290][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.290][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.291][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.292][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.292][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.293][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.294][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.295][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.295][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.296][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.297][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.297][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.298][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.299][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.300][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.300][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.301][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.302][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.302][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.303][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.304][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.304][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.305][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.306][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.307][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.307][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.308][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.309][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.309][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.310][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.311][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.312][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.312][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.313][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.314][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.315][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.315][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.316][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.317][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.318][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.318][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.319][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.320][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.320][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.321][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.322][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.322][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.323][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.324][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.325][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.325][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.326][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.327][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.328][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.328][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.329][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.330][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.331][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.331][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.332][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.333][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.333][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.334][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.335][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.336][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.336][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.337][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.338][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.338][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.339][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.340][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.340][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.341][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.342][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.343][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.343][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.344][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.345][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.346][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.347][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.347][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.348][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:20.349][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:20.349][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.350][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.351][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.352][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.352][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.353][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.354][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.354][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.355][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.356][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.356][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.357][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.358][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.359][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.359][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.360][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.361][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.362][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.363][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.363][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.364][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.365][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.366][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.366][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.367][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.368][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.368][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.369][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.370][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.370][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.371][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.372][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.372][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.373][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.374][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.374][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.375][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.376][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.377][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.377][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.378][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.379][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.380][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.380][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.381][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:20.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.391][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.394][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.397][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.409][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.409][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.412][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.415][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.418][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.434][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.437][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.457][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.460][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.463][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.475][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.478][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.481][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.487][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [19804, 0, 19804, C27H44O7, InChI=1S/C27H44O7/c1-23(2,32)8-5-9-26(33,15-28)22-7-11-27(34)17-12-19(29)18-13-20(30)21(31)14-24(18,3)16(17)6-10-25(22,27)4/h12,16,18,20-22,28,30-34H,5-11,13-15H2,1-4H3/t16-,18-,20+,21-,22-,24+,25+,26+,27+/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:20.488][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:20.488][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:20.490][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.497][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:20.500][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:20.502][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:20.503][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26d0872875c47c33e8205aa7124e0486". biodb.TRACE[2024-06-29 16:04:20.504][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:20.505][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content". biodb.DEBUG[2024-06-29 16:04:20.507][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.513][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:20.523][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.531][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:20.541][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.547][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:20.558][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.564][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:20.574][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.582][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:20.592][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.599][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:20.609][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.616][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:20.626][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.634][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:20.645][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:20.648][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:20.649][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-06-29 16:04:20.650][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:20.651][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-06-29 16:04:20.653][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.659][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:20.670][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.681][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:20.691][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.698][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:20.708][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:20.709][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:20.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:20.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:20.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:20.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:20.716][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:20.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:20.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.723][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.726][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.734][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.737][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.752][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.754][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.769][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.772][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.781][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.784][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.787][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.790][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.793][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:20.794][private$selectFields] biodb.TRACE[2024-06-29 16:04:20.795][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:20.796][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:20.796][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:20.797][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.798][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.798][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.799][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.800][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.801][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.802][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.802][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.803][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.804][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.805][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.805][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.806][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.807][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.807][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.808][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.809][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.810][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.811][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.811][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.812][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.813][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.813][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.814][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.815][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.816][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.816][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.817][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.818][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.819][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.819][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.820][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.821][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.822][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.822][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.823][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.824][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.825][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.825][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.826][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.827][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.827][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.828][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.829][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.830][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.830][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.831][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.832][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.832][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.833][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.834][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.835][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.835][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.836][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.837][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.838][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.838][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.839][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.840][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.841][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.841][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.842][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.843][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.844][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.844][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.845][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.846][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.847][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.847][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.848][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.849][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.849][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.850][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.851][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.852][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.852][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.853][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.854][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.855][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.855][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.856][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.857][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.857][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.858][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.859][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.860][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.860][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.861][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.862][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.863][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.863][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.864][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.865][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.866][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.866][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.867][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.868][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.869][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.869][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.870][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.871][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.871][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:20.872][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.873][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.873][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:20.874][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:20.875][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.876][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.876][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.877][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.878][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.879][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.879][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.880][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.881][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.881][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.882][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.883][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.884][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.884][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.885][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.886][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.886][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.887][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.888][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.888][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.889][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.890][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.891][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.891][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.892][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.893][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.894][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.894][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.895][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.896][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.896][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.897][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.898][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.899][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.900][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.900][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.901][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.902][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.902][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.903][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.904][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:20.905][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:20.905][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.906][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.907][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:20.907][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:20.908][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.909][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.909][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:20.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:20.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:20.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.926][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.929][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.932][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:20.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:20.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:20.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.944][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.949][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:20.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:20.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.952][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.958][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:20.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:20.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.966][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:20.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:20.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.970][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.972][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.975][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:20.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:20.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:20.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.996][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:20.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:20.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:20.999][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:20.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.001][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.016][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.019][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.022][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.028][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [7799, 0, 7799, C16H31N2O8P, InChI=1S/C16H28N2O4.H3O4P/c1-5-12(6-2)22-14-9-11(16(20)21-7-3)8-13(17)15(14)18-10(4)19;1-5(2,3)4/h9,12-15H,5-8,17H2,1-4H3,(H,18,19);(H3,1,2,3,4)/t13-,14+,15+;/m0./s1, ...]. biodb.DEBUG[2024-06-29 16:04:21.029][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:21.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:21.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:21.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:21.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:21.036][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:21.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:21.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.043][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.046][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.058][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.072][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.075][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.090][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.093][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.101][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.104][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.107][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.109][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.113][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:21.113][private$selectFields] biodb.TRACE[2024-06-29 16:04:21.114][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:21.115][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:21.115][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:21.116][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.117][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.118][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.118][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.119][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.120][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.120][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.121][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.122][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.122][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.123][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.124][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.125][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.125][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.126][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.127][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.127][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.128][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.129][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.129][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.130][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.131][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.132][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.132][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.133][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.134][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.134][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.135][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.136][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.137][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.138][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.138][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.139][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.140][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.140][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.141][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.142][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.143][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.143][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.144][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.145][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.145][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.146][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.147][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.147][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.148][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.149][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.150][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.150][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.151][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.152][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.152][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.153][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.154][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.155][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.156][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.156][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.157][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.158][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.158][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.159][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.160][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.160][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.161][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.162][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.163][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.164][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.168][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.169][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.170][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.170][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.171][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.172][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.173][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.173][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.174][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.174][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.175][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.176][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.176][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.177][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.178][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.179][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.179][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.180][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.181][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.182][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.182][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.183][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.184][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.184][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.185][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.186][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.187][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.187][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.188][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.188][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.189][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.190][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.191][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.191][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.192][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.193][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.194][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.194][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:21.195][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:21.196][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.196][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.197][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.198][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.198][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.199][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.200][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.201][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.201][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.202][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.203][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.203][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.204][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.205][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.205][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.206][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.207][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.208][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.208][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.209][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.210][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.211][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.211][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.212][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.212][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.213][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.214][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.214][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.215][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.216][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.217][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.217][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.218][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.219][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.219][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.220][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.221][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.221][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.222][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.223][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.223][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.224][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.225][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.225][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.226][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:21.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.236][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.239][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.242][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.253][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.256][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.259][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.276][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.297][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.300][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.302][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.315][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.317][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.320][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.327][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [71954, 0, 71954, C18H21F3N6O2, InChI=1S/C18H21F3N6O2/c19-18(20,21)13-9-15(22)23-11-12(13)14-10-16(26-1-5-28-6-2-26)25-17(24-14)27-3-7-29-8-4-27/h9-11H,1-8H2,(H2,22,23), ...]. biodb.DEBUG[2024-06-29 16:04:21.327][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:21.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:21.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:21.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:21.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:21.335][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:21.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:21.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.342][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.345][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.354][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.357][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.372][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.375][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.389][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.392][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.401][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.409][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.412][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.415][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.418][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:21.419][private$selectFields] biodb.TRACE[2024-06-29 16:04:21.419][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:21.420][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:21.421][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:21.422][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.422][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.423][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.424][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.425][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.425][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.426][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.427][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.427][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.428][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.429][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.430][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.431][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.431][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.432][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.433][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.433][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.434][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.435][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.436][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.436][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.437][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.438][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.439][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.439][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.440][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.441][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.441][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.442][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.443][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.444][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.444][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.445][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.446][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.447][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.447][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.448][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.449][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.450][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.450][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.451][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.452][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.453][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.453][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.454][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.455][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.455][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.456][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.457][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.457][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.458][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.459][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.459][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.460][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.461][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.461][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.462][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.463][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.464][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.465][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.465][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.466][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.467][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.467][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.468][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.469][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.470][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.470][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.471][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.472][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.473][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.473][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.474][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.475][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.475][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.476][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.477][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.478][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.478][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.479][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.480][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.481][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.481][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.482][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.482][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.483][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.484][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.485][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.485][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.486][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.487][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.487][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.488][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.489][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.489][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.490][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.491][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.491][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.492][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.493][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.494][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.495][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:21.495][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.496][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.497][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:21.497][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:21.498][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.499][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.499][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.500][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.501][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.501][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.502][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.503][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.503][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.504][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.505][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.505][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.506][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.507][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.508][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.508][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.509][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.510][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.510][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.511][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.512][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.512][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.513][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.514][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.514][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.515][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.516][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.517][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.517][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.518][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.519][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.520][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.520][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.521][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.522][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.523][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.523][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.524][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.525][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.526][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.526][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.527][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.528][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.529][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.530][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:21.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.540][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.543][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.546][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.564][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.605][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.608][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.611][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.623][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.626][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.629][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.636][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [197612, 0, 197612, C18H18O9S, InChI=1S/C18H18O9S/c1-7-3-9(19)13-11(4-7)27-16-8(14(13)21)5-12(28-16)18(25,17(24)26-2)6-10(20)15(22)23/h3-4,10,12,19-20,25H,5-6H2,1-2H3,(H,22,23)/t10-,12+,18?/m1/s1, ...]. biodb.DEBUG[2024-06-29 16:04:21.637][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:21.637][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-06-29 16:04:21.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:21.684][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:21.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:21.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:21.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:21.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:21.691][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:21.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:21.694][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:21.696][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:21.697][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-06-29 16:04:21.698][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:21.699][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-06-29 16:04:21.702][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:21.704][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:21.705][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-06-29 16:04:21.706][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:21.707][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-06-29 16:04:21.708][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:21.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:21.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:21.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:21.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:21.715][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:21.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:21.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:21.725][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:21.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:21.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:21.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:21.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:21.732][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:21.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:21.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:21.750][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:21.751][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:21.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:21.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:21.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:21.759][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:21.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:21.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:21.769][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:21.770][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:21.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:21.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:21.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:21.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:21.776][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:21.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:21.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.784][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.787][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.796][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.799][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.808][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.811][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.814][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.816][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.831][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.834][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.837][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.843][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.846][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.849][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:21.850][private$selectFields] biodb.TRACE[2024-06-29 16:04:21.850][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:21.851][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:21.852][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:21.853][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.853][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.854][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.855][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.855][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.856][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.857][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.858][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.858][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.859][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.860][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.861][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.862][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.862][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.863][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.864][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.864][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.865][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.866][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.866][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.867][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.868][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.869][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.870][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.870][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.871][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.872][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.873][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.873][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.874][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.875][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.875][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.876][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.877][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.878][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.879][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.879][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.880][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.881][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.881][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.882][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.883][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.884][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.884][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.885][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.886][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.887][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.887][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.888][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.889][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.890][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.891][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.891][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.892][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.893][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.894][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.895][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.895][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.896][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.897][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.898][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.899][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.899][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.900][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.901][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.901][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.902][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.903][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.903][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.904][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.905][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.906][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.907][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.907][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.908][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.909][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.910][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.910][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.911][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.912][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.917][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.918][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.919][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.920][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.920][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.921][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.922][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.923][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.924][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.924][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.925][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.926][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.926][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.927][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.928][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.929][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.930][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:21.930][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:21.931][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.932][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.933][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.934][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.934][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.935][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.936][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.937][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.938][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.939][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.940][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.940][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.941][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:21.942][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:21.943][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.943][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.944][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:21.945][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:21.946][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.947][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.947][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:21.948][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:21.949][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.950][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.950][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.951][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:21.952][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.953][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.954][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.954][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:21.955][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.956][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.957][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.958][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:21.959][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.960][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.961][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:21.962][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:21.962][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.963][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.964][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:21.965][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:21.965][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.966][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.967][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:21.968][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:21.969][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.970][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.970][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:21.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:21.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:21.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.983][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.986][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.989][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:21.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:21.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:21.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:21.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:21.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.000][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.003][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.006][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.020][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.026][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.029][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.033][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.054][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.057][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.060][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.072][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.075][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.078][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.086][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4648, 0, 4648, C30H50, InChI=1S/C30H50/c1-20(2)21-12-17-27(5)22(21)13-18-29(7)24(27)10-11-25-28(6)16-9-15-26(3,4)23(28)14-19-30(25,29)8/h21-25H,1,9-19H2,2-8H3/t21-,22+,23+,24-,25-,27+,28+,29-,30-/m1/s1, ...]. biodb.DEBUG[2024-06-29 16:04:22.086][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:22.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:22.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:22.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:22.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:22.094][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:22.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:22.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.102][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.105][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.114][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.117][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.129][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.132][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.135][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.150][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.153][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.156][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.162][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.165][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.172][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:22.173][private$selectFields] biodb.TRACE[2024-06-29 16:04:22.174][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:22.175][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:22.175][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:22.176][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.177][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.178][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.178][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.179][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.180][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.180][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.181][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.182][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.182][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.183][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.184][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.184][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.185][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.186][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.186][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.187][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.188][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.189][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.189][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.190][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.191][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.192][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.193][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.193][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.194][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.195][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.195][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.196][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.197][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.198][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.198][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.199][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.200][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.201][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.201][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.202][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.203][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.203][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.204][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.205][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.206][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.206][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.207][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.208][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.208][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.209][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.210][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.210][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.211][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.212][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.213][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.214][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.214][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.215][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.216][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.216][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.217][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.218][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.218][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.219][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.220][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.220][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.221][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.222][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.222][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.223][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.224][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.225][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.225][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.226][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.227][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.227][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.228][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.229][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.229][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.230][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.231][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.231][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.232][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.233][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.233][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.234][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.235][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.235][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.236][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.237][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.237][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.238][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.239][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.239][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.240][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.241][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.242][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.243][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.243][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.244][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:22.245][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:22.245][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.246][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.247][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.248][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.248][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.249][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.250][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.251][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.251][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.252][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.253][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.254][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.254][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.255][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.256][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.257][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.257][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.258][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.259][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.260][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.261][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.262][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.262][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.263][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.264][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.265][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.265][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.268][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.268][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.269][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.270][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.270][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.271][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.272][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.273][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.273][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.274][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.275][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.275][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.276][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.277][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.278][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.279][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.279][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.280][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.281][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.282][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.282][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.283][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:22.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.293][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.295][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.299][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.315][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.318][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.321][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.327][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.339][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.342][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.345][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.367][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.370][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.373][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.376][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.386][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.389][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.392][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.399][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [15440, 0, 15440, C30H50, InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3/b27-17+,28-18+,29-23+,30-24+, ...]. biodb.DEBUG[2024-06-29 16:04:22.400][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:22.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:22.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:22.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:22.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:22.407][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:22.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:22.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.415][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.422][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.432][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.435][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.444][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.447][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.450][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.453][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.468][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.471][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.480][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.483][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.486][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:22.487][private$selectFields] biodb.TRACE[2024-06-29 16:04:22.488][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:22.489][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:22.490][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:22.491][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.491][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.492][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.493][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.493][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.494][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.495][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.496][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.497][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.497][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.498][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.499][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.499][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.500][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.501][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.502][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.503][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.503][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.504][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.505][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.505][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.506][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.507][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.508][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.508][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.509][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.510][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.511][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.511][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.512][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.513][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.514][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.514][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.515][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.516][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.516][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.517][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.518][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.519][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.520][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.520][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.521][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.522][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.523][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.523][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.524][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.525][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.526][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.526][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.527][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.528][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.529][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.530][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.530][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.531][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.532][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.533][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.534][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.534][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.535][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.536][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.537][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.537][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.538][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.539][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.540][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.540][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.541][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.542][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.543][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.543][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.544][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.545][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.546][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.547][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.547][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.548][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.549][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.549][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.550][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.551][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.552][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.552][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.553][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.554][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.555][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.555][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.556][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.557][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.558][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.558][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.559][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.560][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.561][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.562][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.562][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.563][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:22.564][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:22.565][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.566][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.566][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.567][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.568][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.568][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.569][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.570][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.571][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.571][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.572][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.573][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.574][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.574][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.575][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.576][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.576][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.577][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.578][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.579][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.580][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.580][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.581][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.582][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.583][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.583][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.584][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.585][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.586][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.586][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.587][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.588][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.588][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.589][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.590][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.591][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.592][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.592][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.593][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.594][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.594][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.595][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.596][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.597][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.598][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:22.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.608][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.611][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.614][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.627][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.631][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.634][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.650][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.683][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.686][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.689][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.702][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.705][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.708][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.715][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [62447, 0, 62447, C30H50, InChI=1S/C30H50/c1-21(2)11-9-12-22(3)23-15-19-29(7)24(23)13-14-26-28(6)18-10-17-27(4,5)25(28)16-20-30(26,29)8/h11,23-26H,3,9-10,12-20H2,1-2,4-8H3/t23-,24-,25+,26-,28+,29-,30-/m1/s1, ...]. biodb.DEBUG[2024-06-29 16:04:22.716][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:22.717][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:22.719][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:22.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:22.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:22.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:22.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:22.726][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:22.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:22.729][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:22.731][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:22.733][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7269bbea581f1e243800f8ee4e0f4fdb". biodb.TRACE[2024-06-29 16:04:22.734][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:22.735][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content". biodb.DEBUG[2024-06-29 16:04:22.736][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:22.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:22.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:22.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:22.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:22.743][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:22.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:22.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:22.754][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:22.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:22.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:22.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:22.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:22.761][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:22.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:22.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:22.772][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:22.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:22.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:22.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:22.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:22.779][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:22.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:22.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:22.790][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:22.791][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:22.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:22.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:22.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:22.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:22.798][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:22.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:22.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.806][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.809][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.819][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.825][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.837][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.840][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.843][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.859][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.862][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.872][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.875][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.878][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:22.879][private$selectFields] biodb.TRACE[2024-06-29 16:04:22.880][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:22.881][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:22.882][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:22.882][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.883][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.884][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.885][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.886][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.886][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.887][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.888][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.889][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.889][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.890][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.891][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.891][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.892][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.893][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.894][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.894][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.895][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.896][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.896][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.897][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.898][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.899][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.900][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.900][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.901][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.902][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.903][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.903][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.904][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.905][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.906][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.906][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.907][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.908][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.909][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.909][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.910][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.911][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.912][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.912][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.913][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.914][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.915][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.915][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.916][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.917][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.917][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.918][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.919][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.920][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.920][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.921][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.922][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.923][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.923][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.924][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.925][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.925][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.926][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.927][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.928][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.928][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.929][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.930][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.930][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.931][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.932][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.933][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.933][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.934][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.935][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.935][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.936][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.937][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.938][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.943][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.946][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.946][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.947][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.948][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.948][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.949][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.950][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.950][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.951][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.952][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.953][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.953][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.954][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.955][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.955][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.956][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.957][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.957][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.958][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.959][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:22.960][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:22.960][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.961][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.962][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.962][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.963][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:22.964][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:22.965][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.965][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.966][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.967][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:22.967][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.968][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.969][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:22.970][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:22.970][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.971][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.972][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:22.973][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:22.973][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.974][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.975][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:22.976][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:22.977][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.977][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.978][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.979][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:22.980][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.980][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.981][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.982][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:22.983][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.983][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.984][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.985][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:22.986][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.986][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.987][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:22.988][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:22.988][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.989][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.990][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:22.990][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:22.991][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.992][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.993][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:22.994][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:22.994][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.995][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:22.996][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:22.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:22.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:22.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:22.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.006][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.008][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.011][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.023][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.029][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.031][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.037][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.048][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.051][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.054][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.074][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.077][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.080][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.092][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.095][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.098][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.105][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4781, 0, 4781, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24+,25-/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:23.106][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:23.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:23.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:23.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:23.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:23.113][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:23.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:23.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.120][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.123][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.132][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.135][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.141][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.150][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.152][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.168][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.171][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.180][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.188][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.191][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:23.192][private$selectFields] biodb.TRACE[2024-06-29 16:04:23.192][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:23.193][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:23.194][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:23.194][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.195][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.196][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.197][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.197][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.198][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.199][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.199][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.200][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.201][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.202][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.202][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.203][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.204][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.205][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.205][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.206][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.207][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.207][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.208][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.209][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.210][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.210][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.211][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.212][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.212][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.213][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.214][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.214][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.215][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.216][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.216][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.217][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.218][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.219][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.219][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.220][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.221][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.222][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.222][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.223][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.224][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.224][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.225][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.226][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.226][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.227][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.228][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.228][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.229][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.230][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.231][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.231][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.232][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.233][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.234][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.234][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.235][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.236][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.236][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.237][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.238][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.239][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.239][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.240][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.241][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.242][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.242][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.243][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.244][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.245][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.245][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.246][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.247][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.248][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.248][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.249][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.250][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.250][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.251][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.252][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.253][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.253][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.254][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.255][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.255][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.256][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.257][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.257][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.258][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.259][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.260][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.261][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.261][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.262][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.263][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.264][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:23.264][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:23.265][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.266][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.267][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.267][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.268][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.269][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.270][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.270][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.271][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.272][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.272][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.273][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.274][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.275][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.275][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.276][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.277][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.278][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.278][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.279][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.280][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.280][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.281][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.282][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.282][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.283][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.284][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.285][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.285][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.286][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.287][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.288][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.288][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.289][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.290][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.290][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.291][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.292][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.292][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.293][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.294][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.295][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.296][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.296][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.297][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:23.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.307][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.310][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.313][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.326][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.329][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.332][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.382][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.385][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.388][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.400][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.403][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.406][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.412][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [91601, 0, 91601, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24?,25?/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:23.413][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:23.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:23.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:23.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:23.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:23.420][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:23.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:23.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.428][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.431][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.445][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.448][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.457][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.460][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.462][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.465][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.480][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.483][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.492][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.495][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.498][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:23.498][private$selectFields] biodb.TRACE[2024-06-29 16:04:23.499][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:23.500][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:23.500][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:23.501][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.502][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.502][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.503][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.504][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.504][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.505][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.506][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.507][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.507][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.508][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.509][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.509][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.510][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.511][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.512][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.512][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.513][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.514][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.515][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.515][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.516][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.517][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.517][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.518][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.519][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.519][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.520][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.521][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.521][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.522][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.523][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.523][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.524][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.525][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.525][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.526][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.527][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.528][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.528][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.529][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.530][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.531][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.531][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.532][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.533][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.533][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.534][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.535][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.536][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.536][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.537][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.538][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.539][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.539][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.540][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.541][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.542][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.542][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.543][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.544][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.544][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.545][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.546][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.547][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.547][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.548][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.549][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.549][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.550][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.551][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.551][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.552][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.553][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.554][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.554][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.555][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.556][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.556][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.557][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.558][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.559][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.559][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.560][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.561][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.561][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.562][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.563][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.564][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.565][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.565][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.566][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.567][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.567][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.568][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.569][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.570][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:23.570][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:23.571][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.572][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.573][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.574][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.574][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.575][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.576][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.577][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.577][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.578][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.579][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.579][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.580][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.581][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.582][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.583][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.583][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.584][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.585][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.585][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.586][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.587][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.588][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.589][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.589][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.590][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.591][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.592][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.593][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.593][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.594][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.595][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.596][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.596][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.597][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.598][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.599][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.599][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.600][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.601][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.601][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.602][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.603][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.604][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.604][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:23.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.614][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.617][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.621][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.633][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.635][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.638][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.645][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.650][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.679][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.682][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.690][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.693][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.703][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.706][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.709][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.715][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [95147, 0, 95147, C29H40N2O4, InChI=1S/C29H40N2O4/c1-3-18-16(2)14-22-20(18)10-11-21-19-6-4-8-26(33)30-13-5-7-24-28(34)27(29(35)31-24)25(32)12-9-17(19)15-23(21)22/h4,8,10-11,16-24,27H,3,5-7,9,12-15H2,1-2H3,(H,30,33)(H,31,35)/t16-,17-,18-,19+,20+,21-,22+,23+,24+,27?/m1/s1, ...]. biodb.DEBUG[2024-06-29 16:04:23.716][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:23.717][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:23.719][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:23.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:23.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:23.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:23.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:23.727][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:23.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:23.729][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:23.732][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:23.733][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-06-29 16:04:23.734][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:23.735][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-06-29 16:04:23.737][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:23.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:23.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:23.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:23.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:23.744][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:23.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:23.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:23.755][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:23.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:23.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:23.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:23.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:23.761][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:23.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:23.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:23.772][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:23.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:23.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:23.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:23.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:23.779][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:23.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:23.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:23.790][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:23.791][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:23.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:23.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:23.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:23.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:23.798][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:23.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:23.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.806][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.809][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.818][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.821][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.837][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.840][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.855][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.858][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.867][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.870][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.873][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:23.874][private$selectFields] biodb.TRACE[2024-06-29 16:04:23.875][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:23.876][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:23.876][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:23.877][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.878][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.879][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.880][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.880][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.881][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.882][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.883][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.883][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.884][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.885][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.886][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.886][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.887][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.888][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.889][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.889][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.890][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.891][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.892][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.892][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.893][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.894][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.895][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.895][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.896][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.897][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.898][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.898][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.899][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.900][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.901][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.901][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.902][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.903][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.904][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.904][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.905][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.906][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.907][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.908][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.908][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.909][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.910][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.911][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.912][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.912][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.913][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.914][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.915][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.916][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.916][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.917][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.918][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.918][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.919][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.920][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.921][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.921][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.922][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.923][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.924][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.924][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.925][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.926][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.927][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.927][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.928][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.929][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.929][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.930][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.935][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.935][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.936][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.937][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.938][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.938][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.939][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.940][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.941][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.941][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.942][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.943][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.944][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.949][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.950][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.951][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.952][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.952][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.953][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.954][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.955][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.955][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.956][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.957][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.958][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.958][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:23.959][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:23.960][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.961][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.961][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.962][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.963][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:23.964][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:23.964][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.965][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.966][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.967][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:23.967][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.968][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.968][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:23.969][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:23.970][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.971][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.971][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:23.972][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:23.973][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.974][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.974][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:23.975][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:23.976][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.976][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.977][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.978][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:23.979][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.979][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.980][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.981][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:23.981][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.982][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.983][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.984][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:23.985][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.985][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.986][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:23.987][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:23.988][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.988][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.989][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:23.990][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:23.990][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.991][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.992][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:23.993][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:23.993][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.994][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.995][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:23.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:23.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:23.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:23.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:23.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.004][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.007][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.010][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.023][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.029][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.032][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.042][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.051][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.054][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.057][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.079][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.082][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.085][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.091][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.097][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.100][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.103][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.110][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [636, 0, 636, C24H26O6, InChI=1S/C24H26O6/c1-12(2)6-7-14-19-17(11-16(26)22(14)28-5)29-18-10-15(25)13-8-9-24(3,4)30-23(13)20(18)21(19)27/h6,10-11,25-26H,7-9H2,1-5H3, ...]. biodb.DEBUG[2024-06-29 16:04:24.111][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:24.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:24.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:24.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:24.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:24.119][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:24.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:24.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.126][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.130][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.138][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.141][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.153][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.156][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.159][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.175][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.178][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.181][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.187][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.190][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.193][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:24.194][private$selectFields] biodb.TRACE[2024-06-29 16:04:24.195][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:24.200][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:24.201][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:24.202][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.204][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.204][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.205][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.206][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.207][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.207][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.208][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.209][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.210][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.211][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.211][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.212][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.213][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.213][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.214][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.215][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.216][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.216][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.217][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.218][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.218][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.219][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.220][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.221][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.221][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.222][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.223][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.224][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.224][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.225][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.226][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.227][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.227][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.228][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.229][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.230][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.230][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.231][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.232][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.233][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.233][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.234][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.235][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.236][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.236][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.237][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.238][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.239][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.239][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.240][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.241][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.242][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.242][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.243][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.244][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.244][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.245][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.246][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.246][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.247][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.248][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.249][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.249][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.250][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.251][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.251][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.252][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.253][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.254][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.254][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.255][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.256][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.256][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.257][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.258][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.259][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.259][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.260][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.261][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.262][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.262][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.263][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.264][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.265][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.265][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.266][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.267][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.268][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.269][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.269][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.270][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.271][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.271][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.272][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.273][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.274][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:24.274][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:24.275][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.276][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.276][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.277][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.278][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.279][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.280][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.280][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.281][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.282][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.282][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.283][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.284][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.285][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.286][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.286][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.287][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.288][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.288][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.289][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.290][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.291][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.291][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.292][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.293][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.293][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.294][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.295][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.296][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.297][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.297][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.298][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.299][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.299][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.300][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.301][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.302][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.302][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.303][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.304][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.304][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.305][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.306][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.307][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.307][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:24.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.316][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.317][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.320][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.323][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.339][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.342][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.351][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.384][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.387][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.390][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.403][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.406][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.409][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.415][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [64199, 0, 64199, C24H27ClN2O2, InChI=1S/C24H26N2O2.ClH/c27-24(28)20-9-10-23-22(16-20)21(17-25-23)8-4-5-13-26-14-11-19(12-15-26)18-6-2-1-3-7-18;/h1-3,6-7,9-11,16-17,25H,4-5,8,12-15H2,(H,27,28);1H, ...]. biodb.DEBUG[2024-06-29 16:04:24.416][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:24.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:24.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:24.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:24.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:24.424][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:24.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:24.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.431][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.434][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.444][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.447][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.457][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.460][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.466][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.469][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.484][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.487][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.495][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.498][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.501][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:24.502][private$selectFields] biodb.TRACE[2024-06-29 16:04:24.503][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:24.503][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:24.504][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:24.505][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.506][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.506][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.507][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.508][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.508][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.509][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.510][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.510][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.511][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.512][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.513][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.514][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.514][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.515][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.516][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.516][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.517][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.518][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.518][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.519][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.520][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.521][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.521][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.522][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.523][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.524][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.524][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.525][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.526][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.526][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.527][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.528][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.529][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.529][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.530][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.531][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.531][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.532][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.533][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.534][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.535][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.535][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.536][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.537][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.537][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.538][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.539][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.540][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.540][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.541][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.542][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.542][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.543][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.544][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.544][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.545][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.546][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.546][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.547][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.548][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.548][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.549][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.550][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.551][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.552][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.552][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.553][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.554][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.554][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.555][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.556][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.557][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.557][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.558][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.559][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.559][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.560][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.561][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.562][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.562][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.563][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.564][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.565][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.566][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.566][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.567][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.568][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.568][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.569][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.570][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.570][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.571][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.572][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.573][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.573][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.574][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:24.575][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:24.576][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.576][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.577][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.578][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.578][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.579][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.580][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.580][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.581][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.582][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.583][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.583][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.584][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.585][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.586][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.586][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.587][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.588][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.589][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.589][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.590][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.591][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.592][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.592][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.593][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.594][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.594][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.595][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.596][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.596][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.597][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.598][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.598][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.599][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.600][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.601][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.602][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.602][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.603][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.604][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.605][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.606][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.606][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.607][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.608][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:24.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.618][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.621][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.624][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.636][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.639][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.641][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.647][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.650][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.660][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.680][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.684][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.689][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.703][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.705][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.709][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.712][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.719][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [65648, 0, 65648, C24H26O6, InChI=1S/C24H26O6/c1-13(2)9-10-23-20(27)22(28-5)11-14-19(26)18-15(25)7-6-8-16(18)29-24(14,23)17(12-22)21(3,4)30-23/h6-9,11,17,25H,10,12H2,1-5H3/t17-,22-,23-,24+/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:24.719][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:24.720][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:24.726][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:24.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:24.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:24.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:24.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:24.733][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:24.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:24.736][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:24.738][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:24.739][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-06-29 16:04:24.740][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:24.741][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-06-29 16:04:24.744][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:24.746][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:24.748][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-06-29 16:04:24.749][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:24.750][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-06-29 16:04:24.751][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:24.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:24.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:24.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:24.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:24.758][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:24.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:24.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:24.768][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:24.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:24.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:24.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:24.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:24.775][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:24.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:24.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:24.786][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:24.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:24.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:24.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:24.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:24.793][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:24.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:24.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:24.803][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:24.805][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:24.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:24.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:24.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:24.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:24.812][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:24.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:24.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.819][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.822][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.832][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.835][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.841][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.844][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.850][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.853][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.869][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.872][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.881][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.884][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.887][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:24.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:24.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.890][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:24.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:24.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.894][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:24.894][private$selectFields] biodb.TRACE[2024-06-29 16:04:24.895][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:24.896][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:24.897][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:24.898][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.898][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.899][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.900][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.900][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.901][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.902][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.903][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.903][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.904][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.919][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.919][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.920][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.921][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.922][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.923][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.923][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.924][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.925][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.925][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.926][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.927][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.928][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.929][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.929][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.930][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.931][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.932][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.933][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.934][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.935][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.935][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.936][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.937][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.938][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.939][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.939][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.940][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.941][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.941][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.942][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.943][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.944][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.945][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.945][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.946][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.947][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.947][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.948][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:24.949][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:24.950][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.951][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.951][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.952][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.953][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.954][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.954][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:24.955][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:24.956][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.957][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.958][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.958][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:24.959][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.960][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.960][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:24.961][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:24.962][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.963][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.968][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:24.970][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:24.971][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.972][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.973][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:24.973][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:24.974][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.975][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.975][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.976][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:24.977][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.978][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.978][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.979][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:24.980][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.981][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.981][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.982][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:24.983][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.983][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.984][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:24.985][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:24.986][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.987][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.987][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:24.988][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:24.989][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.989][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.990][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:24.991][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:24.992][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.992][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.993][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:24.994][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:24.994][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.995][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:24.996][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:24.997][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:24.997][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:24.998][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:24.999][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:24.999][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.000][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.001][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.001][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.002][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.003][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.004][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.005][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.005][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.006][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.007][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.008][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.008][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.009][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.010][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.010][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.011][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.012][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.013][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.014][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.014][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.015][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.016][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.016][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.017][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.018][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.019][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.019][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.020][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.021][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.021][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.022][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.023][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.024][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.025][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.027][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.027][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.028][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.029][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.029][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.030][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.031][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.032][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.032][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.033][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.034][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:25.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.043][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.046][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.050][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.062][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.064][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.067][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.076][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.085][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.088][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.091][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.094][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.116][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.119][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.122][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.128][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.131][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.135][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.138][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.141][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.148][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4648, 0, 4648, C30H50, InChI=1S/C30H50/c1-20(2)21-12-17-27(5)22(21)13-18-29(7)24(27)10-11-25-28(6)16-9-15-26(3,4)23(28)14-19-30(25,29)8/h21-25H,1,9-19H2,2-8H3/t21-,22+,23+,24-,25-,27+,28+,29-,30-/m1/s1, ...]. biodb.DEBUG[2024-06-29 16:04:25.149][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:25.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:25.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:25.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:25.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:25.156][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:25.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:25.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.164][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.167][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.178][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.187][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.193][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.196][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.211][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.219][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.225][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.228][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.231][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.234][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.237][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.240][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:25.240][private$selectFields] biodb.TRACE[2024-06-29 16:04:25.241][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:25.242][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:25.242][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:25.243][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.244][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.245][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.246][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.247][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.248][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.248][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.249][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.249][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.251][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.251][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.252][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.253][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.253][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.254][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.255][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.256][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.257][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.257][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.258][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.259][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.259][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.260][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.261][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.262][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.263][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.263][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.264][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.264][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.265][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.266][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.267][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.267][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.268][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.269][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.270][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.270][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.271][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.272][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.272][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.273][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.274][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.275][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.275][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.276][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.277][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.278][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.278][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.279][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.280][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.281][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.281][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.282][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.283][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.283][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.284][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.285][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.286][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.286][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.287][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.288][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.289][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.289][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.290][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.291][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.292][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.292][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.293][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.294][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.294][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.295][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.296][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.296][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.297][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.298][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.299][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.300][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.300][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.301][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.302][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.302][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.303][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.304][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.304][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.305][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.306][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.306][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.307][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.308][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.309][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.309][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.310][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.311][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.311][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.312][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.313][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.313][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.314][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.315][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.315][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.316][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.317][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.317][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.318][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.319][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:25.320][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:25.320][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.321][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.322][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.322][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.323][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.324][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.325][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.326][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.326][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.327][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.328][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.328][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.329][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.330][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.331][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.331][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.332][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.333][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.334][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.334][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.335][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.336][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.336][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.337][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.338][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.339][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.340][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.340][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.341][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.342][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.342][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.343][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.344][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.345][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.345][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.346][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.347][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.347][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.348][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.349][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.349][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.350][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.351][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.352][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.353][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.353][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.354][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.357][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.358][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:25.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.368][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.371][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.374][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.387][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.390][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.393][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.396][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.414][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.418][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.421][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.442][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.445][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.448][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.465][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.468][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.471][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.477][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [15440, 0, 15440, C30H50, InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3/b27-17+,28-18+,29-23+,30-24+, ...]. biodb.DEBUG[2024-06-29 16:04:25.478][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:25.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:25.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:25.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:25.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:25.485][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:25.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:25.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.493][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.496][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.505][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.508][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.517][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.520][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.523][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.525][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.540][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.543][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.552][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.555][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.558][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.564][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:25.564][private$selectFields] biodb.TRACE[2024-06-29 16:04:25.565][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:25.566][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:25.566][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:25.567][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.568][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.569][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.569][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.570][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.571][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.571][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.572][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.573][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.574][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.574][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.575][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.576][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.577][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.578][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.578][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.579][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.580][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.580][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.581][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.582][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.582][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.583][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.584][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.584][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.585][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.586][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.587][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.587][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.588][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.589][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.589][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.590][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.591][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.592][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.593][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.594][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.594][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.595][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.596][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.596][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.597][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.598][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.598][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.599][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.600][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.601][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.601][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.602][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.603][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.604][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.605][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.605][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.606][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.607][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.607][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.608][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.609][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.610][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.610][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.611][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.612][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.612][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.613][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.614][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.614][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.615][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.616][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.617][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.618][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.618][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.619][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.620][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.621][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.621][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.622][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.623][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.623][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.624][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.625][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.625][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.626][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.627][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.627][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.628][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.629][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.629][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.630][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.631][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.632][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.633][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.633][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.634][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.635][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.636][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.636][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.637][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.638][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.639][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.639][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.640][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.641][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.641][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.642][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.643][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:25.644][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:25.644][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.645][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.646][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.646][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.648][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.649][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.649][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.650][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.651][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.652][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.652][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.653][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.654][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.654][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.655][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.656][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.656][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.657][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.658][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.658][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.659][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.660][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.660][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.661][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.662][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.663][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.663][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.664][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.665][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.666][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.667][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.667][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.668][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.669][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.670][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.670][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.671][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.672][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.672][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.673][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.674][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.674][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.675][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.676][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.677][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:25.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.687][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.690][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.693][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.710][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.713][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.715][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.718][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.730][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.754][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.757][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.760][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.772][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.775][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.778][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.785][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [62447, 0, 62447, C30H50, InChI=1S/C30H50/c1-21(2)11-9-12-22(3)23-15-19-29(7)24(23)13-14-26-28(6)18-10-17-27(4,5)25(28)16-20-30(26,29)8/h11,23-26H,3,9-10,12-20H2,1-2,4-8H3/t23-,24-,25+,26-,28+,29-,30-/m1/s1, ...]. biodb.DEBUG[2024-06-29 16:04:25.786][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:25.786][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:25.789][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:25.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:25.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:25.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:25.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:25.796][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:25.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:25.799][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:25.801][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:25.802][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7269bbea581f1e243800f8ee4e0f4fdb". biodb.TRACE[2024-06-29 16:04:25.804][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:25.805][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content". biodb.DEBUG[2024-06-29 16:04:25.807][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:25.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:25.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:25.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:25.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:25.814][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:25.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:25.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:25.824][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:25.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:25.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:25.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:25.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:25.831][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:25.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:25.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:25.842][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:25.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:25.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:25.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:25.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:25.849][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:25.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:25.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:25.860][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:25.861][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:25.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:25.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:25.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:25.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:25.868][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:25.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:25.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.876][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.879][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.888][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.891][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.905][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.908][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.924][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.927][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.933][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.936][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.939][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.942][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.945][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.948][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:25.949][private$selectFields] biodb.TRACE[2024-06-29 16:04:25.950][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:25.950][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:25.951][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:25.952][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.952][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.953][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.954][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.955][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:25.960][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:25.961][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.962][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.963][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.964][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:25.964][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.965][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.966][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:25.966][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:25.967][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.968][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.968][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:25.969][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:25.970][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.971][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.972][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:25.972][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:25.973][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.974][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.975][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.975][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:25.976][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.977][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.977][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.978][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:25.979][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.980][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.980][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.981][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:25.982][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.982][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.985][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:25.986][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:25.986][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.987][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.988][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:25.989][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:25.989][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.990][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.991][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:25.992][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:25.992][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.993][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.994][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.994][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:25.995][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.996][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:25.996][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:25.998][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:25.998][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:25.999][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.000][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.000][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.001][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.002][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.003][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.003][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.004][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.005][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.005][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.006][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.007][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.007][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.008][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.009][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.009][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.010][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.011][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.012][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.013][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.013][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.014][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.015][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.016][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.016][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.017][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.018][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.018][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.019][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.020][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.021][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.021][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.022][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.023][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.024][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.024][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.025][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.026][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.027][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.027][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.028][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.029][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.030][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.030][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.031][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.032][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.032][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.033][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.034][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.035][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:26.036][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:26.036][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.037][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.038][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.038][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.039][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.040][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.041][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.041][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.042][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.043][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.043][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.044][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.045][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.045][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.046][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.047][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.047][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.049][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.049][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.050][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.051][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.051][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.052][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.053][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.054][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.054][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.055][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.056][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.056][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.057][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.058][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.058][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.059][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.060][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.061][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.062][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.062][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.063][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.064][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.065][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.065][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.066][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.067][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.067][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.068][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.069][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.070][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.070][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.071][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:26.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.081][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.084][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.087][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.100][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.103][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.106][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.109][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.115][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.128][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.131][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.134][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.157][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.160][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.162][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.169][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.175][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.178][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.181][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.189][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4781, 0, 4781, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24+,25-/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:26.190][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:26.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:26.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:26.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:26.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:26.197][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:26.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:26.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.204][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.226][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.235][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.241][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.244][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.250][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.253][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.256][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.270][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.274][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.282][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.285][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.288][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.291][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.294][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:26.295][private$selectFields] biodb.TRACE[2024-06-29 16:04:26.296][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:26.296][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:26.297][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:26.298][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.298][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.299][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.300][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.300][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.301][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.302][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.302][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.303][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.304][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.305][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.306][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.306][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.307][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.308][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.309][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.309][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.310][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.311][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.312][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.312][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.313][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.314][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.314][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.315][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.316][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.316][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.317][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.318][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.319][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.320][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.320][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.321][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.322][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.322][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.323][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.324][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.325][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.325][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.326][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.327][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.328][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.328][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.329][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.330][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.330][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.331][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.332][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.332][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.333][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.334][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.334][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.335][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.336][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.337][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.337][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.338][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.339][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.340][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.341][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.341][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.342][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.343][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.343][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.344][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.345][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.346][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.346][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.347][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.348][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.349][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.349][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.350][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.351][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.351][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.352][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.353][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.354][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.355][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.355][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.356][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.357][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.358][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.358][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.359][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.374][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.375][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.375][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.376][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.377][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.377][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.378][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.379][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.379][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.380][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.381][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.381][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.382][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.383][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.384][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.384][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.385][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.386][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.387][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.388][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:26.389][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:26.390][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.391][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.391][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.392][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.393][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.393][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.394][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.395][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.396][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.397][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.397][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.398][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.399][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.400][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.400][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.401][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.402][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.403][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.403][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.404][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.405][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.406][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.406][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.407][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.408][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.409][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.410][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.411][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.414][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.414][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.415][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.416][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.417][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.417][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.418][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.419][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.420][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.421][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.421][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.422][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.423][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.423][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.424][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.425][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.426][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:26.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.437][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.441][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.444][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.456][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.462][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.475][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.481][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.492][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.507][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.510][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.513][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.516][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.525][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.528][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.531][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.538][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [91601, 0, 91601, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24?,25?/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:26.538][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:26.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:26.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:26.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:26.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:26.546][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:26.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:26.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.553][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.556][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.565][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.582][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.585][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.600][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.603][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.613][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.616][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.619][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.622][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.625][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:26.626][private$selectFields] biodb.TRACE[2024-06-29 16:04:26.626][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:26.627][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:26.628][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:26.629][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.629][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.630][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.631][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.631][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.632][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.633][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.634][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.634][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.635][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.636][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.636][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.637][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.638][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.639][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.639][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.640][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.641][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.642][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.642][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.643][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.644][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.645][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.645][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.646][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.647][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.647][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.648][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.649][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.650][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.650][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.651][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.652][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.653][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.653][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.654][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.655][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.656][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.656][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.657][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.658][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.659][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.659][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.660][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.661][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.662][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.663][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.663][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.664][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.665][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.665][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.666][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.667][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.667][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.669][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.670][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.670][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.671][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.672][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.672][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.673][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.674][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.674][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.675][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.676][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.676][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.677][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.678][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.678][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.679][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.680][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.680][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.681][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.682][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.683][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.683][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.684][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.685][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.685][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.686][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.687][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.687][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.688][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.689][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.690][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.691][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.691][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.692][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.693][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.694][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.694][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.695][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.696][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.697][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.697][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.698][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.699][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.699][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.700][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.701][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.702][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.703][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:26.703][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.704][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.705][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:26.706][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:26.706][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.707][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.708][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.708][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.709][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.710][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.711][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.711][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.712][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.713][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.713][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.714][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.715][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.716][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.717][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.717][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.718][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.719][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.720][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.720][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.721][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.722][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.723][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.723][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.724][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.725][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.725][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.726][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.727][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.728][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.729][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.730][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.730][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.731][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.732][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.737][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.738][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.739][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.739][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.740][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.741][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.742][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.743][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.743][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.744][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:26.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.754][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.757][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.760][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.771][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.777][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.780][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.789][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.792][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.816][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.819][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.822][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.827][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.834][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.837][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.840][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:26.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:26.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.847][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [95147, 0, 95147, C29H40N2O4, InChI=1S/C29H40N2O4/c1-3-18-16(2)14-22-20(18)10-11-21-19-6-4-8-26(33)30-13-5-7-24-28(34)27(29(35)31-24)25(32)12-9-17(19)15-23(21)22/h4,8,10-11,16-24,27H,3,5-7,9,12-15H2,1-2H3,(H,30,33)(H,31,35)/t16-,17-,18-,19+,20+,21-,22+,23+,24+,27?/m1/s1, ...]. biodb.DEBUG[2024-06-29 16:04:26.847][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:26.848][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-06-29 16:04:26.850][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:26.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:26.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:26.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:26.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:26.858][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:26.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-29 16:04:26.860][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-06-29 16:04:26.863][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-29 16:04:26.864][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-06-29 16:04:26.865][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-29 16:04:26.866][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-06-29 16:04:26.868][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:26.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:26.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:26.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:26.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:26.875][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:26.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:26.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:26.886][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:26.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:26.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:26.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:26.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:26.893][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:26.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:26.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:26.903][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:26.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:26.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:26.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:26.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:26.910][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:26.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:26.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-29 16:04:26.921][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-06-29 16:04:26.923][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:26.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:26.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:26.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:26.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:26.929][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:26.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:26.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:26.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:26.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.937][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.940][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:26.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:26.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:26.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.949][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.952][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:26.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:26.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.958][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:26.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:26.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:26.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:26.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.967][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.970][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:26.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:26.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:26.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.990][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.993][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:26.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:26.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:26.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:26.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:26.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:26.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.002][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.005][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.008][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.011][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.013][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:27.014][private$selectFields] biodb.TRACE[2024-06-29 16:04:27.015][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:27.015][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:27.016][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:27.017][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.018][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.019][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.019][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.020][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.021][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.021][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.022][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.023][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.024][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.024][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.025][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.026][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.026][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.027][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.028][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.028][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.029][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.030][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.031][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.031][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.032][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.033][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.033][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.034][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.035][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.036][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.036][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.038][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.039][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.040][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.040][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.041][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.042][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.042][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.043][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.044][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.044][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.045][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.046][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.047][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.048][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.048][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.049][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.050][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.051][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.051][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.052][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.053][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.053][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.054][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.055][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.055][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.056][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.057][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.058][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.059][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.059][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.060][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.061][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.061][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.062][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.063][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.064][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.064][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.065][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.066][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.067][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.067][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.068][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.069][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.069][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.070][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.071][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.072][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.072][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.073][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.074][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.075][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.075][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.076][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.077][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.078][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.078][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.079][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.080][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.080][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.081][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.082][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.083][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.084][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.084][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.085][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.086][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.086][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.087][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.088][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.089][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.089][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.090][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.091][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.091][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.092][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.093][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.094][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:27.095][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:27.095][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.096][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.097][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.097][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.098][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.099][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.100][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.100][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.101][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.102][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.102][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.103][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.104][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.105][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.105][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.106][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.107][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.107][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.108][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.109][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.109][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.110][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.111][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.112][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.112][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.113][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.114][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.115][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.115][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.116][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.117][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.118][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.118][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.119][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.120][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.121][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.121][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.122][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.123][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.124][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.125][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.125][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.126][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.127][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.127][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.128][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.129][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.129][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.130][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:27.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.143][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.145][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.149][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.161][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.164][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.167][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.187][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.190][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.193][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.196][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.219][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.223][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.226][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.244][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.247][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.250][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.257][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [636, 0, 636, C24H26O6, InChI=1S/C24H26O6/c1-12(2)6-7-14-19-17(11-16(26)22(14)28-5)29-18-10-15(25)13-8-9-24(3,4)30-23(13)20(18)21(19)27/h6,10-11,25-26H,7-9H2,1-5H3, ...]. biodb.DEBUG[2024-06-29 16:04:27.258][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:27.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:27.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:27.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:27.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:27.266][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:27.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:27.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.274][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.277][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.287][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.290][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.293][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.296][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.306][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.309][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.325][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.328][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.337][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.338][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.341][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.344][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.348][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.351][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:27.352][private$selectFields] biodb.TRACE[2024-06-29 16:04:27.353][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:27.353][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:27.354][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:27.355][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.356][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.356][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.357][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.358][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.359][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.359][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.360][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.361][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.362][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.363][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.363][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.364][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.365][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.366][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.367][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.367][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.368][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.369][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.370][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.371][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.372][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.372][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.373][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.374][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.375][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.376][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.376][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.377][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.378][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.379][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.380][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.380][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.381][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.382][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.383][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.384][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.385][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.385][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.386][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.387][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.388][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.388][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.389][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.390][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.391][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.392][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.392][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.393][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.394][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.395][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.395][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.396][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.397][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.398][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.399][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.399][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.400][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.401][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.402][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.414][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.415][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.416][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.417][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.418][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.418][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.419][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.420][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.421][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.422][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.422][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.423][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.424][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.425][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.426][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.426][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.427][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.428][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.429][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.430][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.431][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.432][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.433][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.434][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.435][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.436][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.436][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.437][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.438][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.439][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.439][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.440][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.441][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.442][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.443][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.443][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.444][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.445][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.446][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.446][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.447][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.448][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.449][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.449][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.450][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:27.451][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:27.452][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.453][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.453][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.454][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.455][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.456][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.457][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.457][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.458][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.459][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.460][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.460][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.461][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.462][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.463][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.464][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.465][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.466][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.466][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.467][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.468][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.469][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.469][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.470][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.471][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.471][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.472][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.473][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.474][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.475][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.475][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.476][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.477][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.478][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.478][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.479][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.480][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.481][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.482][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.482][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.483][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.484][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.485][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.486][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.486][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:27.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.497][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.500][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.504][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.522][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.526][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.535][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.542][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.570][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.573][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.577][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.590][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.593][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.603][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [64199, 0, 64199, C24H27ClN2O2, InChI=1S/C24H26N2O2.ClH/c27-24(28)20-9-10-23-22(16-20)21(17-25-23)8-4-5-13-26-14-11-19(12-15-26)18-6-2-1-3-7-18;/h1-3,6-7,9-11,16-17,25H,4-5,8,12-15H2,(H,27,28);1H, ...]. biodb.DEBUG[2024-06-29 16:04:27.604][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-29 16:04:27.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:27.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:27.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:27.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:27.611][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:27.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-29 16:04:27.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.619][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.623][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.632][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.635][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.639][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.645][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.653][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.656][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.673][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.676][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.686][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.689][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.693][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.697][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.701][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:27.702][private$selectFields] biodb.TRACE[2024-06-29 16:04:27.702][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-06-29 16:04:27.703][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-06-29 16:04:27.704][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-06-29 16:04:27.705][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.706][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.707][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.708][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.709][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.710][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.711][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.712][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.713][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.714][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.715][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.715][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.717][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.718][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.718][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.719][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.720][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.721][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.722][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.723][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.724][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.725][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.726][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.727][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.727][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.728][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.729][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.730][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.731][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.732][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.733][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.734][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.735][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.736][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.737][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.738][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.739][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.739][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.740][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.741][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.742][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.743][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.743][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.744][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.745][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.746][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.747][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.748][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.749][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.750][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.750][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.751][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.752][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.753][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.754][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.755][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.755][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.756][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.757][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.758][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.759][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.760][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.761][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.762][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.763][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.764][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.765][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.765][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.766][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.767][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.768][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.769][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.769][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.770][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.771][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.772][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.773][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.774][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-29 16:04:27.774][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.775][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.776][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.777][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.778][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.778][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.779][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.780][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.781][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.782][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.782][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.783][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.784][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.785][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.786][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.787][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.788][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.789][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.790][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.796][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.797][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.798][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.799][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.800][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-06-29 16:04:27.801][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.801][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.802][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:27.803][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-06-29 16:04:27.804][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.805][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.806][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.807][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.808][ef$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.809][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.810][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.810][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.811][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.812][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.813][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.814][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.815][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.815][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.816][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.817][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.818][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.819][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.819][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.820][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.821][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.822][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.823][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.824][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.824][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.825][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.826][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.827][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.828][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.829][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.829][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.830][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.831][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.832][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.832][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.833][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.834][ef$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.835][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.836][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.836][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.837][ef$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.838][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.839][ef$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.840][ef$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.841][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-06-29 16:04:27.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-29 16:04:27.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-29 16:04:27.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.852][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.855][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.858][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-06-29 16:04:27.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-06-29 16:04:27.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-29 16:04:27.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.873][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.877][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.880][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-29 16:04:27.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-29 16:04:27.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-29 16:04:27.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-29 16:04:27.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-29 16:04:27.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-29 16:04:27.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-29 16:04:27.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-29 16:04:27.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.927][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.930][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.933][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-06-29 16:04:27.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-06-29 16:04:27.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.938][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-29 16:04:27.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-29 16:04:27.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.948][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.952][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.955][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-06-29 16:04:27.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-06-29 16:04:27.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.974][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [65648, 0, 65648, C24H26O6, InChI=1S/C24H26O6/c1-13(2)9-10-23-20(27)22(28-5)11-14-19(26)18-15(25)7-6-8-16(18)29-24(14,23)17(12-22)21(3,4)30-23/h6-9,11,17,25H,10,12H2,1-5H3/t17-,22-,23-,24+/m0/s1, ...]. biodb.DEBUG[2024-06-29 16:04:27.975][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-06-29 16:04:27.976][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-06-29 16:04:27.980][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:04:27.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:04:27.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.983][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:04:27.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:04:27.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-29 16:04:27.986][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-29 16:04:27.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-29 16:04:27.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-29 16:04:27.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-29 16:04:27.992][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-06-29 16:04:27.994][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler biodb.INFO [2024-06-29 16:04:27.994][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2024-06-29 16:04:27.996][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-06-29 16:04:27.998][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-29 16:04:27.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-29 16:04:28.000][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-06-29 16:04:28.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-29 16:04:28.002][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-06-29 16:04:28.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1395 ] > > proc.time() user system elapsed 54.336 2.834 167.103
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbChebi_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbChebi.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’ * checking for file ‘biodbChebi/DESCRIPTION’ ... OK * this is package ‘biodbChebi’ version ‘1.11.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘biodbChebi’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... SKIPPED * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in ‘longtests’ ... OK * checking tests in ‘longtests’ ... Running ‘testthat.R’ OK * DONE Status: OK
biodbChebi.Rcheck/00install.out
* installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)