Back to Long Tests report for BioC 3.19

This page was generated on 2024-07-13 23:55 -0400 (Sat, 13 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 12/33HostnameOS / ArchCHECK
biodbNci 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-07-13 09:55 -0400 (Sat, 13 Jul 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_19
git_last_commit: 0db4525
git_last_commit_date: 2024-04-30 11:41:04 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.4 Monterey / x86_64  OK  

CHECK results for biodbNci on nebbiolo1

To the developers/maintainers of the biodbNci package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbNci
Version: 1.8.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
StartedAt: 2024-07-13 16:05:21 -0400 (Sat, 13 Jul 2024)
EndedAt: 2024-07-13 16:06:24 -0400 (Sat, 13 Jul 2024)
EllapsedTime: 63.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-07-13 16:06:21.303][biodb::testContext]
biodb.INFO [2024-07-13 16:06:21.305][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:06:21.306][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-07-13 16:06:21.306][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:06:21.307][biodb::testContext]
biodb.INFO [2024-07-13 16:06:21.313][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:06:21.315][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-13 16:06:21.322][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:06:21.323][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-13 16:06:21.324][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-13 16:06:21.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.328][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-13 16:06:21.344][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-13 16:06:21.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.347][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-13 16:06:21.348][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-13 16:06:21.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.351][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-13 16:06:21.352][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-13 16:06:21.353][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-13 16:06:21.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.357][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-13 16:06:21.357][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-13 16:06:21.358][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-13 16:06:21.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.362][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-13 16:06:21.363][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-13 16:06:21.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.366][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-13 16:06:21.367][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-13 16:06:21.368][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-13 16:06:21.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.371][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-13 16:06:21.372][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-13 16:06:21.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.375][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-13 16:06:21.376][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-13 16:06:21.377][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-13 16:06:21.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.380][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:06:21.381][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-13 16:06:21.382][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-13 16:06:21.383][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-13 16:06:21.384][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-13 16:06:21.385][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-13 16:06:21.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.388][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-13 16:06:21.389][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-13 16:06:21.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.392][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-13 16:06:21.393][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-13 16:06:21.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.396][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-13 16:06:21.397][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-13 16:06:21.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.401][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-13 16:06:21.402][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-13 16:06:21.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.405][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-13 16:06:21.406][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-13 16:06:21.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.409][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:06:21.410][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-13 16:06:21.413][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-13 16:06:21.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.416][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-13 16:06:21.417][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-13 16:06:21.418][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-13 16:06:21.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.424][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-13 16:06:21.459][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.472][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-13 16:06:21.473][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.474][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:06:21.475][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.476][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.478][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.479][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.480][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:06:21.481][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:06:21.482][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.483][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-13 16:06:21.483][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:06:21.484][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.485][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.486][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:06:21.486][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:06:21.486][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:06:21.486][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:06:21.486][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:06:21.487][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:06:21.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:21.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:21.490][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:06:21.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:21.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:21.492][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.493][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.494][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:06:21.495][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:06:21.496][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.496][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.497][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-13 16:06:21.499][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.500][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:06:21.501][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.502][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:06:21.503][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.504][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.504][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.505][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.506][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:06:21.507][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:06:21.508][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.509][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-13 16:06:21.510][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:06:21.511][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.512][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.512][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:06:21.512][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:06:21.512][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:06:21.512][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:06:21.512][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:06:21.513][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:06:21.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:21.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:21.516][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:06:21.517][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:21.518][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:21.519][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.519][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.520][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:06:21.521][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:06:21.522][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.523][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.524][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-13 16:06:21.525][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.526][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-13 16:06:21.527][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.528][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:06:21.529][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.530][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.531][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.532][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.533][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:06:21.533][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:06:21.534][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.535][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-13 16:06:21.536][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:06:21.537][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.538][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.539][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.540][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:06:21.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:21.541][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:21.542][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:06:21.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:21.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:21.545][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.546][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.547][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:06:21.547][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:06:21.548][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.549][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.550][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-13 16:06:21.552][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.553][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:06:21.553][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.554][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:06:21.555][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.556][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.557][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.558][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.559][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:06:21.560][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:06:21.561][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.562][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-13 16:06:21.562][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:06:21.563][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.564][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.565][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.566][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:06:21.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:21.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:21.569][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:06:21.569][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:21.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:21.571][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.572][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.573][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:06:21.574][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:06:21.574][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.575][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.579][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:06:21.580][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.653][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-13 16:06:21.658][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-13 16:06:21.659][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-13 16:06:21.660][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-13 16:06:21.661][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-13 16:06:21.663][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-13 16:06:21.664][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-13 16:06:21.665][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-13 16:06:21.666][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-13 16:06:21.668][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-13 16:06:21.669][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-13 16:06:21.670][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-13 16:06:21.671][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-13 16:06:21.673][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-13 16:06:21.674][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-13 16:06:21.675][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-13 16:06:21.676][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-13 16:06:21.678][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-13 16:06:21.679][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-13 16:06:21.680][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-13 16:06:21.681][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-13 16:06:21.683][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-13 16:06:21.684][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-13 16:06:21.685][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-13 16:06:21.686][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-13 16:06:21.688][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-13 16:06:21.689][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-13 16:06:21.690][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-13 16:06:21.691][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-13 16:06:21.693][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-13 16:06:21.694][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-13 16:06:21.695][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-13 16:06:21.696][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-13 16:06:21.698][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-13 16:06:21.699][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-13 16:06:21.700][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-13 16:06:21.701][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-13 16:06:21.702][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-13 16:06:21.704][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-13 16:06:21.705][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-13 16:06:21.706][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-13 16:06:21.707][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-13 16:06:21.709][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-13 16:06:21.710][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-13 16:06:21.711][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-13 16:06:21.717][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-13 16:06:21.718][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-13 16:06:21.720][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-13 16:06:21.721][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-13 16:06:21.722][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-13 16:06:21.724][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-13 16:06:21.725][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-13 16:06:21.727][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-13 16:06:21.728][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-13 16:06:21.729][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-13 16:06:21.731][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-13 16:06:21.732][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-13 16:06:21.734][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-13 16:06:21.735][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-13 16:06:21.737][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-13 16:06:21.738][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-13 16:06:21.739][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-13 16:06:21.741][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-13 16:06:21.742][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-13 16:06:21.744][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-13 16:06:21.745][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-13 16:06:21.746][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-13 16:06:21.748][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-13 16:06:21.749][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-13 16:06:21.750][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-13 16:06:21.752][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-13 16:06:21.753][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-13 16:06:21.755][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-13 16:06:21.756][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-13 16:06:21.757][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-13 16:06:21.758][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-13 16:06:21.760][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-13 16:06:21.761][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-13 16:06:21.763][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-13 16:06:21.764][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-13 16:06:21.765][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-13 16:06:21.767][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-13 16:06:21.768][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-13 16:06:21.787][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-13 16:06:21.789][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:06:21.792][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:06:21.793][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.795][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:21.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:21.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:21.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:21.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:21.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:21.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:21.903][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-07-13 16:06:21.912][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-07-13 16:06:21.913][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.914][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-07-13 16:06:21.915][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.916][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:06:21.917][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.918][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-07-13 16:06:21.919][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.920][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.921][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-07-13 16:06:21.921][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:06:21.922][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.923][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-07-13 16:06:21.924][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:06:21.925][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-07-13 16:06:21.925][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-07-13 16:06:21.925][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-07-13 16:06:21.925][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-07-13 16:06:21.925][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-07-13 16:06:21.925][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-07-13 16:06:21.925][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-07-13 16:06:21.926][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:21.927][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.928][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-13 16:06:21.929][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:21.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:21.930][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:06:21.931][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:21.932][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:21.933][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:06:21.934][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-13 16:06:21.934][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-13 16:06:21.934][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-07-13 16:06:21.934][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-07-13 16:06:21.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:06:21.936][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:06:21.936][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:21.937][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:21.943][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-07-13 16:06:21.967][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-07-13 16:06:21.968][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-07-13 16:06:21.972][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-07-13 16:06:21.976][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-07-13 16:06:21.981][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:06:21.981][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:06:21.983][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:06:21.984][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:06:21.985][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:06:21.986][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-07-13 16:06:21.995][biodb::testThat]
biodb.INFO [2024-07-13 16:06:21.996][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-13 16:06:21.996][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:21.997][biodb::testThat]
biodb.TRACE[2024-07-13 16:06:22.000][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-07-13 16:06:22.002][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-07-13 16:06:22.005][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-07-13 16:06:22.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:06:22.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:22.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:22.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:22.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:22.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:22.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-13 16:06:22.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.064][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.090][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.118][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.121][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.162][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:06:22.216][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-07-13 16:06:22.218][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:06:22.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:06:22.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.222][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:06:22.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:06:22.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.225][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:06:22.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:06:22.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.229][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:06:22.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:06:22.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.259][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.292][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.296][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.300][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.319][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.320][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.322][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.340][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.343][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.344][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.346][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.347][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.367][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.368][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.370][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.384][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.387][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.391][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.392][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.393][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.403][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.417][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.418][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.420][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.430][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.431][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.433][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.437][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.438][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.439][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.443][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.444][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.445][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.449][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.450][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.452][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.455][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.456][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.458][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.472][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-07-13 16:06:22.503][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-07-13 16:06:22.504][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-07-13 16:06:22.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:06:22.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:22.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:22.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:22.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:22.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:22.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-13 16:06:22.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.547][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.550][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.554][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.602][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.610][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.614][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.621][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:06:22.646][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-07-13 16:06:22.667][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:06:22.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:06:22.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.671][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:06:22.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:06:22.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.674][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:06:22.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:06:22.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.678][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:06:22.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:06:22.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.689][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.718][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.722][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.725][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:22.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.753][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.754][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.755][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.766][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.769][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.776][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.780][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.781][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.783][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.784][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.805][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.806][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.808][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.819][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.823][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.827][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.830][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.832][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.833][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.834][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.856][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.857][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.859][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.873][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.877][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.881][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.882][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.883][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.904][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.908][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.910][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.920][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:22.921][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:22.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.923][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.926][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.927][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:06:22.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.929][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.933][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:22.934][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:22.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.935][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.939][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:22.940][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:22.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.941][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.945][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.946][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:22.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.948][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.951][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.952][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:22.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.954][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:22.957][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:22.958][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:22.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:22.960][ef$get] fields variable is a list.
biodb.INFO [2024-07-13 16:06:22.966][biodb::testThat]
biodb.INFO [2024-07-13 16:06:22.967][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-13 16:06:22.968][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:22.968][biodb::testThat]
biodb.DEBUG[2024-07-13 16:06:22.970][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-07-13 16:06:22.977][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-07-13 16:06:22.981][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-07-13 16:06:22.983][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-07-13 16:06:22.984][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-07-13 16:06:22.985][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-07-13 16:06:22.987][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2024-07-13 16:06:22.988][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-07-13 16:06:22.989][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-07-13 16:06:22.990][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-07-13 16:06:22.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:06:22.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:22.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:22.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:22.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:22.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:22.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-13 16:06:23.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.013][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:23.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:23.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.017][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:23.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:23.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:23.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:23.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:23.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:23.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:23.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:23.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.032][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:23.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:23.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:23.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:23.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:23.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:23.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.048][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.051][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.058][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:06:23.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:06:23.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-13 16:06:23.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.096][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:06:23.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:06:23.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.100][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:06:23.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:06:23.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.104][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:23.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:23.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.107][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:06:23.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:06:23.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:23.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:23.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:23.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:06:23.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.119][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:23.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:23.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:23.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:23.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:23.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:23.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.130][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:23.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:23.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:23.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:23.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:23.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:23.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.140][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:23.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:23.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:23.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:23.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.148][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:06:23.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:06:23.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.152][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:23.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:23.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:06:23.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:06:23.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.160][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.163][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.173][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:06:23.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:06:23.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:06:23.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:06:23.209][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-07-13 16:06:23.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-13 16:06:23.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-13 16:06:23.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:06:23.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:06:23.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:06:23.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:06:23.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-13 16:06:23.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-13 16:06:23.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:06:23.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:06:23.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:06:23.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:06:23.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-13 16:06:23.239][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.240][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-13 16:06:23.241][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:23.242][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.247][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.248][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-13 16:06:23.248][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:23.249][biodb::testThat]
biodb.WARN [2024-07-13 16:06:23.268][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-07-13 16:06:23.287][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-07-13 16:06:23.294][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.295][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-13 16:06:23.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:23.297][biodb::testThat]
biodb.TRACE[2024-07-13 16:06:23.316][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:06:23.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:06:23.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.320][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:06:23.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:06:23.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.324][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:06:23.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:06:23.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:06:23.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:06:23.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.359][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:06:23.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:06:23.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.362][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:06:23.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:06:23.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.366][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:06:23.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:06:23.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:06:23.369][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:06:23.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:06:23.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:23.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-13 16:06:23.376][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.377][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-13 16:06:23.378][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:23.379][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.385][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.386][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-13 16:06:23.386][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:23.387][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.396][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.397][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-13 16:06:23.398][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:23.399][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.403][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.404][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-13 16:06:23.405][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:23.406][biodb::testThat]
biodb.INFO [2024-07-13 16:06:23.410][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-13 16:06:23.412][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-07-13 16:06:23.413][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-07-13 16:06:23.413][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-13 16:06:23.414][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.416][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.417][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-13 16:06:23.426][biodb::testContext]
biodb.INFO [2024-07-13 16:06:23.427][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:06:23.428][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-07-13 16:06:23.429][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:06:23.429][biodb::testContext]
biodb.INFO [2024-07-13 16:06:23.431][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:06:23.433][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-13 16:06:23.436][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:06:23.437][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-13 16:06:23.438][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-13 16:06:23.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.441][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-13 16:06:23.442][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-13 16:06:23.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.445][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-13 16:06:23.446][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-13 16:06:23.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.450][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-13 16:06:23.450][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-13 16:06:23.451][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-13 16:06:23.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.455][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-13 16:06:23.456][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-13 16:06:23.456][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-13 16:06:23.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.460][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-13 16:06:23.461][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-13 16:06:23.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.464][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-13 16:06:23.465][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-13 16:06:23.466][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-13 16:06:23.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.469][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-13 16:06:23.470][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-13 16:06:23.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.473][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-13 16:06:23.474][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-13 16:06:23.475][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-13 16:06:23.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.478][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:06:23.479][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-13 16:06:23.480][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-13 16:06:23.481][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-13 16:06:23.482][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-13 16:06:23.483][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-13 16:06:23.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.486][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-13 16:06:23.487][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-13 16:06:23.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.490][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-13 16:06:23.491][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-13 16:06:23.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.494][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-13 16:06:23.495][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-13 16:06:23.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.499][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-13 16:06:23.499][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-13 16:06:23.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.503][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-13 16:06:23.504][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-13 16:06:23.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.507][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:06:23.508][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-13 16:06:23.511][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-13 16:06:23.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.514][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-13 16:06:23.515][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-13 16:06:23.516][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-13 16:06:23.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.523][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-13 16:06:23.524][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.525][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-13 16:06:23.526][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.527][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:06:23.528][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.529][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.530][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.530][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.531][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:06:23.532][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:06:23.533][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.534][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-13 16:06:23.535][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:06:23.536][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.537][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.538][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:06:23.538][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:06:23.538][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:06:23.538][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:06:23.538][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:06:23.539][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:06:23.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:23.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:23.541][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:06:23.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:23.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:23.544][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.545][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.545][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:06:23.546][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:06:23.547][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.548][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.549][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-13 16:06:23.551][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.551][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:06:23.552][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.553][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:06:23.554][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.555][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.556][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.557][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.558][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:06:23.559][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:06:23.560][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.560][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-13 16:06:23.561][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:06:23.562][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.563][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.564][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:06:23.564][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:06:23.564][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:06:23.564][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:06:23.564][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:06:23.565][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:06:23.566][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:23.567][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:23.567][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:06:23.568][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:23.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:23.570][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.571][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.572][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:06:23.573][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:06:23.573][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.574][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.575][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-13 16:06:23.577][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.578][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-13 16:06:23.579][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.579][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:06:23.580][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.582][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.583][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.584][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:06:23.585][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:06:23.586][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.587][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-13 16:06:23.587][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:06:23.588][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.589][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.590][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.591][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:06:23.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:23.593][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:23.594][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:06:23.594][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:23.595][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:23.596][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.597][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.598][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:06:23.599][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:06:23.600][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.600][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.601][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-13 16:06:23.603][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.604][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:06:23.605][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.606][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:06:23.607][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.607][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.608][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.609][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.610][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:06:23.611][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:06:23.612][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.613][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-13 16:06:23.614][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:06:23.615][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.615][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.616][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.617][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:06:23.618][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:23.619][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:23.620][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:06:23.621][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:23.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:23.622][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.623][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.624][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:06:23.625][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:06:23.626][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.627][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.628][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:06:23.628][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.701][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-13 16:06:23.703][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-13 16:06:23.704][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-13 16:06:23.705][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-13 16:06:23.706][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-13 16:06:23.708][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-13 16:06:23.709][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-13 16:06:23.710][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-13 16:06:23.711][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-13 16:06:23.712][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-13 16:06:23.714][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-13 16:06:23.715][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-13 16:06:23.716][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-13 16:06:23.717][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-13 16:06:23.719][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-13 16:06:23.720][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-13 16:06:23.721][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-13 16:06:23.722][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-13 16:06:23.724][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-13 16:06:23.725][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-13 16:06:23.726][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-13 16:06:23.727][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-13 16:06:23.729][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-13 16:06:23.730][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-13 16:06:23.731][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-13 16:06:23.732][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-13 16:06:23.734][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-13 16:06:23.735][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-13 16:06:23.736][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-13 16:06:23.737][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-13 16:06:23.739][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-13 16:06:23.740][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-13 16:06:23.741][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-13 16:06:23.742][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-13 16:06:23.743][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-13 16:06:23.745][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-13 16:06:23.746][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-13 16:06:23.747][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-13 16:06:23.748][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-13 16:06:23.750][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-13 16:06:23.751][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-13 16:06:23.752][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-13 16:06:23.753][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-13 16:06:23.755][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-13 16:06:23.759][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-13 16:06:23.760][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-13 16:06:23.762][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-13 16:06:23.763][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-13 16:06:23.764][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-13 16:06:23.765][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-13 16:06:23.767][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-13 16:06:23.768][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-13 16:06:23.769][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-13 16:06:23.770][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-13 16:06:23.772][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-13 16:06:23.773][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-13 16:06:23.774][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-13 16:06:23.775][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-13 16:06:23.777][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-13 16:06:23.778][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-13 16:06:23.779][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-13 16:06:23.780][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-13 16:06:23.782][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-13 16:06:23.783][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-13 16:06:23.784][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-13 16:06:23.785][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-13 16:06:23.786][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-13 16:06:23.788][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-13 16:06:23.789][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-13 16:06:23.790][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-13 16:06:23.791][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-13 16:06:23.793][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-13 16:06:23.794][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-13 16:06:23.795][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-13 16:06:23.796][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-13 16:06:23.798][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-13 16:06:23.799][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-13 16:06:23.800][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-13 16:06:23.801][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-13 16:06:23.803][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-13 16:06:23.804][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-13 16:06:23.805][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-13 16:06:23.806][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-13 16:06:23.808][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-13 16:06:23.809][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:06:23.810][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:06:23.811][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.812][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:06:23.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:06:23.912][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-07-13 16:06:23.914][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-07-13 16:06:23.915][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.916][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-07-13 16:06:23.917][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.918][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:06:23.919][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.920][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-07-13 16:06:23.921][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.921][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.922][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-07-13 16:06:23.923][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:06:23.924][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.925][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-07-13 16:06:23.926][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:06:23.927][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-07-13 16:06:23.927][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-07-13 16:06:23.927][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-07-13 16:06:23.927][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-07-13 16:06:23.927][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-07-13 16:06:23.927][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-07-13 16:06:23.927][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-07-13 16:06:23.928][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-13 16:06:23.929][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.930][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-13 16:06:23.931][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:23.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:23.932][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:06:23.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:06:23.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:06:23.935][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:06:23.936][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-13 16:06:23.936][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-13 16:06:23.936][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-07-13 16:06:23.936][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-07-13 16:06:23.936][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:06:23.937][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:06:23.938][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-13 16:06:23.939][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:06:23.940][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-07-13 16:06:23.943][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-07-13 16:06:23.944][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-07-13 16:06:23.945][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-07-13 16:06:23.946][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-07-13 16:06:23.947][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:06:23.948][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:06:23.949][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:06:23.950][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:06:23.951][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:06:23.952][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-07-13 16:06:23.953][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-13 16:06:23.954][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-07-13 16:06:23.955][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-07-13 16:06:23.956][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-13 16:06:23.957][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:06:23.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:06:23.958][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:06:23.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:06:23.960][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:06:23.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  4.056   0.234   4.281

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: OK

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)