Pierrick Roger
| Snapshot Date: 2024-06-30 14:00 -0400 (Sun, 30 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_19 |
| git_last_commit: fad38a4 |
| git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-03 10:22 -0400 (Wed, 03 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4480 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4511 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4469 |
| 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 200/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.10.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. |
| Package: biodbChebi |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.10.0.tar.gz |
| StartedAt: 2024-07-01 12:52:37 -0400 (Mon, 01 Jul 2024) |
| EndedAt: 2024-07-01 12:54:01 -0400 (Mon, 01 Jul 2024) |
| EllapsedTime: 84.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.10.0’
* 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 ‘biodbChebi’ can be installed ... OK
* 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 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-07-01 12:53:26.533][biodb::testContext]
biodb.INFO [2024-07-01 12:53:26.539][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-01 12:53:26.540][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-07-01 12:53:26.541][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-01 12:53:26.543][biodb::testContext]
biodb.INFO [2024-07-01 12:53:26.553][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-01 12:53:26.556][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-01 12:53:26.568][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:26.569][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-01 12:53:26.570][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-01 12:53:26.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:26.575][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-01 12:53:26.595][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-01 12:53:26.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.599][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[2024-07-01 12:53:26.600][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-01 12:53:26.601][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-01 12:53:26.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:26.604][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-01 12:53:26.605][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-01 12:53:26.606][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-01 12:53:26.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.624][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[2024-07-01 12:53:26.625][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-01 12:53:26.626][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-01 12:53:26.627][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-01 12:53:26.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:26.630][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-01 12:53:26.631][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-01 12:53:26.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.633][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[2024-07-01 12:53:26.634][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-01 12:53:26.635][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-01 12:53:26.636][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-01 12:53:26.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:26.639][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-01 12:53:26.640][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-01 12:53:26.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.642][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[2024-07-01 12:53:26.642][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-01 12:53:26.643][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-01 12:53:26.644][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-01 12:53:26.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:26.647][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-01 12:53:26.648][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-01 12:53:26.649][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-01 12:53:26.650][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-01 12:53:26.650][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-01 12:53:26.651][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-01 12:53:26.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.654][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[2024-07-01 12:53:26.655][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-01 12:53:26.655][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-01 12:53:26.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:26.658][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-01 12:53:26.659][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-01 12:53:26.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.661][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[2024-07-01 12:53:26.662][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-01 12:53:26.663][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-01 12:53:26.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:26.666][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-01 12:53:26.667][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-01 12:53:26.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.669][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[2024-07-01 12:53:26.670][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-01 12:53:26.671][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-01 12:53:26.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:26.674][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-01 12:53:26.675][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-01 12:53:26.693][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-01 12:53:26.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.696][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[2024-07-01 12:53:26.697][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-01 12:53:26.698][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-01 12:53:26.699][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-01 12:53:26.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:26.706][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-01 12:53:26.744][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.760][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-01 12:53:26.762][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.763][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:26.765][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.767][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.769][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-01 12:53:26.770][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:26.771][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.771][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-01 12:53:26.772][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:26.773][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.774][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.775][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:26.775][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:26.775][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:26.775][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-01 12:53:26.775][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-01 12:53:26.776][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:26.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:26.777][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:26.778][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:26.779][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:26.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:26.780][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.781][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.782][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:26.783][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:26.783][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.784][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.785][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-01 12:53:26.787][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.788][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-01 12:53:26.789][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.790][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:26.790][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.791][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.792][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.793][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.794][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-01 12:53:26.794][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:26.795][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.796][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-01 12:53:26.797][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:26.798][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.799][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.799][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:26.799][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:26.799][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:26.799][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-01 12:53:26.799][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-01 12:53:26.800][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:26.801][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:26.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:26.803][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:26.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:26.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:26.805][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.806][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.806][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:26.807][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:26.808][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.809][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.810][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-01 12:53:26.811][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.812][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-01 12:53:26.813][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.814][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:26.815][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.815][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.816][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.817][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.818][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-01 12:53:26.826][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:26.827][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.828][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-01 12:53:26.828][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:26.829][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.830][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.831][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.832][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:26.832][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:26.833][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:26.834][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:26.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:26.835][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:26.836][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.837][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.838][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:26.838][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:26.839][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.840][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.841][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-01 12:53:26.843][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.844][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-01 12:53:26.845][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.845][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:26.846][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.847][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.848][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.849][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.849][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-01 12:53:26.850][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:26.851][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.852][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-01 12:53:26.852][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:26.853][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.854][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:26.855][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.856][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:26.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:26.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:26.858][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:26.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:26.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:26.860][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:26.861][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.862][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:26.862][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:26.863][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:26.864][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:26.869][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:26.870][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.870][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[2024-07-01 12:53:26.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.874][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[2024-07-01 12:53:26.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.878][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[2024-07-01 12:53:26.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.881][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[2024-07-01 12:53:26.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.885][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[2024-07-01 12:53:26.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.888][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[2024-07-01 12:53:26.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.892][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[2024-07-01 12:53:26.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.895][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[2024-07-01 12:53:26.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.899][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[2024-07-01 12:53:26.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.902][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[2024-07-01 12:53:26.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.906][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[2024-07-01 12:53:26.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.909][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[2024-07-01 12:53:26.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.913][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[2024-07-01 12:53:26.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.916][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[2024-07-01 12:53:26.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.920][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[2024-07-01 12:53:26.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.923][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[2024-07-01 12:53:26.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.927][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[2024-07-01 12:53:26.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:26.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:26.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:26.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:26.930][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[2024-07-01 12:53:26.931][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-01 12:53:26.937][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-01 12:53:26.938][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-01 12:53:26.939][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-01 12:53:26.941][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-01 12:53:26.942][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-01 12:53:26.943][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-01 12:53:26.944][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-01 12:53:26.945][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-01 12:53:26.946][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-01 12:53:26.947][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-01 12:53:26.949][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-01 12:53:26.950][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-01 12:53:26.951][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-01 12:53:26.952][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-01 12:53:26.953][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-01 12:53:26.954][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-01 12:53:26.956][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-01 12:53:26.957][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-01 12:53:26.958][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-01 12:53:26.959][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-01 12:53:26.961][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-01 12:53:26.962][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-01 12:53:26.963][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-01 12:53:26.964][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-01 12:53:26.965][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-01 12:53:26.966][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-01 12:53:26.967][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-01 12:53:26.968][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-01 12:53:26.970][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-01 12:53:26.971][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-01 12:53:26.972][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-01 12:53:26.973][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-01 12:53:26.975][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-01 12:53:26.976][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-01 12:53:26.977][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-01 12:53:26.978][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-01 12:53:26.979][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-01 12:53:26.980][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-01 12:53:26.981][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-01 12:53:26.983][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-01 12:53:26.984][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-01 12:53:26.985][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-01 12:53:26.986][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-01 12:53:26.994][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-01 12:53:26.995][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-01 12:53:26.996][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-01 12:53:26.997][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-01 12:53:26.999][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-01 12:53:27.000][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-01 12:53:27.001][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-01 12:53:27.002][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-01 12:53:27.003][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-01 12:53:27.004][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-01 12:53:27.006][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-01 12:53:27.007][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-01 12:53:27.008][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-01 12:53:27.009][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-01 12:53:27.010][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-01 12:53:27.011][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-01 12:53:27.013][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-01 12:53:27.014][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-01 12:53:27.015][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-01 12:53:27.016][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-01 12:53:27.017][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-01 12:53:27.018][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-01 12:53:27.020][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-01 12:53:27.021][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-01 12:53:27.022][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-01 12:53:27.023][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-01 12:53:27.024][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-01 12:53:27.026][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-01 12:53:27.027][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-01 12:53:27.028][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-01 12:53:27.029][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-01 12:53:27.030][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-01 12:53:27.031][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-01 12:53:27.033][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-01 12:53:27.034][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-01 12:53:27.035][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-01 12:53:27.036][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-01 12:53:27.037][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-01 12:53:27.038][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-01 12:53:27.044][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-01 12:53:27.046][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-01 12:53:27.051][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:27.052][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.053][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.054][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[2024-07-01 12:53:27.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.064][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[2024-07-01 12:53:27.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.069][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[2024-07-01 12:53:27.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.074][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[2024-07-01 12:53:27.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.079][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[2024-07-01 12:53:27.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.084][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[2024-07-01 12:53:27.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.089][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[2024-07-01 12:53:27.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.094][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[2024-07-01 12:53:27.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.099][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[2024-07-01 12:53:27.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.104][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[2024-07-01 12:53:27.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.109][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[2024-07-01 12:53:27.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.114][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[2024-07-01 12:53:27.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.119][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[2024-07-01 12:53:27.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.124][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[2024-07-01 12:53:27.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.129][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[2024-07-01 12:53:27.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.134][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[2024-07-01 12:53:27.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.139][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[2024-07-01 12:53:27.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:27.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.144][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[2024-07-01 12:53:27.146][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-01 12:53:27.163][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-01 12:53:27.165][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:27.166][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-01 12:53:27.167][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:27.168][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:27.169][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:27.170][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:27.170][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:27.171][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-01 12:53:27.172][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-01 12:53:27.173][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:27.174][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:27.174][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-01 12:53:27.175][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:27.176][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-01 12:53:27.176][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-01 12:53:27.176][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-01 12:53:27.176][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-01 12:53:27.176][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-01 12:53:27.176][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-01 12:53:27.176][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-01 12:53:27.176][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-01 12:53:27.176][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-01 12:53:27.176][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-01 12:53:27.176][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-01 12:53:27.177][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:27.178][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:27.178][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:27.178][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:27.179][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-01 12:53:27.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:27.180][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:27.181][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:27.182][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:27.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:27.183][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:27.184][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:27.184][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-01 12:53:27.185][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:27.186][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:27.187][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:27.187][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-01 12:53:27.187][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-01 12:53:27.194][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-01 12:53:27.196][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-01 12:53:27.197][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-01 12:53:27.198][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-01 12:53:27.200][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-01 12:53:27.201][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-01 12:53:27.233][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-01 12:53:27.234][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-01 12:53:27.240][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-01 12:53:27.245][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-01 12:53:27.251][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-01 12:53:27.252][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-01 12:53:27.254][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-01 12:53:27.255][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-01 12:53:27.268][biodb::testThat]
biodb.INFO [2024-07-01 12:53:27.269][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-07-01 12:53:27.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:27.271][biodb::testThat]
biodb.TRACE[2024-07-01 12:53:27.276][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-07-01 12:53:27.278][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:27.283][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:27.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:27.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:27.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:27.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:27.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:27.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:27.317][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[2024-07-01 12:53:27.330][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.331][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.333][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.351][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:27.352][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:27.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.354][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.381][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:27.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:27.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.385][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:27.386][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:27.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.387][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.389][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:27.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:27.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.392][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:27.407][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:27.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.409][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:27.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:27.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.413][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:27.414][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:27.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.416][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:27.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:27.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.420][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.421][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.423][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.424][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.429][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:27.430][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.432][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.434][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:27.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.438][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.439][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.441][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.446][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:27.447][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:27.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.448][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:27.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:27.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.453][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:27.454][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.455][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.456][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:27.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.461][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:27.462][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:27.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.464][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.465][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:27.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:27.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:27.536][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-07-01 12:53:27.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:27.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:27.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:27.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:27.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:27.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:27.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:27.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:27.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.633][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-01 12:53:27.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-01 12:53:27.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.636][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-01 12:53:27.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-01 12:53:27.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.640][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-01 12:53:27.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-01 12:53:27.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.643][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-01 12:53:27.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-01 12:53:27.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.748][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.749][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.751][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:27.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:27.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.783][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.784][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.786][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:27.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:27.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:27.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:27.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:27.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:27.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:27.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.811][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:27.812][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:27.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.814][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.815][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:27.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:27.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.827][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:27.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:27.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.831][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:27.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:27.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.834][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:27.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:27.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.838][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:27.839][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:27.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.840][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.841][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:27.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:27.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.864][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.865][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.867][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:27.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.890][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.891][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.893][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:27.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.907][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:27.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:27.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.912][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:27.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:27.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.916][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:27.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:27.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.919][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:27.927][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:27.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.929][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.930][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:27.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:27.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.942][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.946][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.950][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.953][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.954][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.956][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.957][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:27.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.969][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.973][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.976][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.979][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.980][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.982][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.983][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:27.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.994][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:27.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:27.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:27.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:27.998][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:27.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:28.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.002][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:28.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:28.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.005][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:28.006][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:28.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.008][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.009][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:28.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:28.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.021][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.031][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.032][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.034][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:28.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:28.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:28.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:28.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:28.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:28.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.057][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:28.058][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:28.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.059][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.060][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:28.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:28.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.073][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:28.074][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:28.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.076][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.082][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:28.090][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:28.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.092][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.097][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:28.098][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:28.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.100][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.105][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:28.106][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:28.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.108][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.113][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.114][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.115][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.120][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:28.121][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:28.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.123][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.128][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:28.129][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:28.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.130][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.135][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:28.136][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:28.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.138][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.143][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-01 12:53:28.144][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:28.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.146][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.151][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:28.153][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:28.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.155][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.161][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:28.163][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:28.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.164][ef$get] fields variable is a list.
biodb.INFO [2024-07-01 12:53:28.173][biodb::testThat]
biodb.INFO [2024-07-01 12:53:28.174][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-01 12:53:28.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:28.176][biodb::testThat]
biodb.DEBUG[2024-07-01 12:53:28.191][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-07-01 12:53:28.201][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:28.206][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-07-01 12:53:28.208][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:28.209][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-07-01 12:53:28.211][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:28.234][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:28.236][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:28.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:28.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:28.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:28.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:28.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:28.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:28.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:28.250][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:28.251][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:28.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.252][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:28.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:28.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.281][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:28.283][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:28.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.284][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.286][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:28.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:28.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.289][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:28.290][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:28.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.291][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.293][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:28.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:28.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.296][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:28.297][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:28.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.298][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.300][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:28.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:28.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.303][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.304][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.305][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:28.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.310][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:28.311][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:28.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.312][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.313][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:28.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:28.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.317][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:28.318][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:28.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.319][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.320][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:28.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:28.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.324][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:28.325][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:28.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.326][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:28.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:28.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.331][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:28.332][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:28.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.333][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.334][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:28.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:28.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.338][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:28.339][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:28.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.341][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.342][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:28.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:28.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.346][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:28.347][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:28.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.348][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.349][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:28.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:28.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:28.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:28.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:28.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:28.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:28.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:28.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:28.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:28.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:28.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:28.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:28.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:28.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:28.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:28.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:28.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:28.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:28.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:28.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:28.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:28.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:28.385][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-07-01 12:53:28.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-01 12:53:28.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-01 12:53:28.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-01 12:53:28.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-01 12:53:28.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-01 12:53:28.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-01 12:53:28.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-01 12:53:28.412][biodb::testThat]
biodb.INFO [2024-07-01 12:53:28.414][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-01 12:53:28.414][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:28.415][biodb::testThat]
biodb.TRACE[2024-07-01 12:53:28.419][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:28.420][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:28.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.422][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:28.423][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-07-01 12:53:28.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:28.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:28.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:28.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:28.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:28.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:28.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:28.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:28.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:28.466][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-07-01 12:53:28.472][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-01 12:53:28.494][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:28.510][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-01 12:53:28.511][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:28.513][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-01 12:53:28.537][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:28.541][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:28.542][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:28.543][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:28.908][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:29.313][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:29.316][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-07-01 12:53:29.332][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-07-01 12:53:29.335][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-07-01 12:53:29.350][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:29.351][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:29.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.353][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.354][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:29.355][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:29.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.372][ef$get] fields variable is a list.
biodb.INFO [2024-07-01 12:53:29.377][biodb::testThat]
biodb.INFO [2024-07-01 12:53:29.378][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-07-01 12:53:29.379][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:29.380][biodb::testThat]
biodb.TRACE[2024-07-01 12:53:29.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:29.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:29.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:29.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:29.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:29.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:29.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:29.477][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:29.481][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:29.482][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-01 12:53:29.483][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:29.485][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-07-01 12:53:29.510][biodb::testThat]
biodb.INFO [2024-07-01 12:53:29.512][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-07-01 12:53:29.513][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:29.514][biodb::testThat]
biodb.TRACE[2024-07-01 12:53:29.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:29.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:29.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:29.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:29.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:29.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:29.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:29.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:29.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:29.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:29.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:29.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:29.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-01 12:53:29.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-01 12:53:29.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.563][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-01 12:53:29.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-01 12:53:29.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.566][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-01 12:53:29.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-01 12:53:29.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.569][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-01 12:53:29.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-01 12:53:29.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.592][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:29.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:29.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:29.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:29.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:29.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:29.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:29.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:29.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:29.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:29.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:29.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:29.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.613][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-01 12:53:29.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-01 12:53:29.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.623][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-01 12:53:29.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-01 12:53:29.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.627][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-01 12:53:29.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-01 12:53:29.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:29.630][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-01 12:53:29.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-01 12:53:29.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:29.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-01 12:53:29.641][biodb::testThat]
biodb.INFO [2024-07-01 12:53:29.642][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-01 12:53:29.643][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:29.644][biodb::testThat]
biodb.INFO [2024-07-01 12:53:29.653][biodb::testThat]
biodb.INFO [2024-07-01 12:53:29.654][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-01 12:53:29.655][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:29.656][biodb::testThat]
biodb.INFO [2024-07-01 12:53:29.666][biodb::testThat]
biodb.INFO [2024-07-01 12:53:29.667][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-01 12:53:29.668][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:29.669][biodb::testThat]
biodb.DEBUG[2024-07-01 12:53:29.673][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-07-01 12:53:30.140][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-07-01 12:53:30.418][biodb::testThat]
biodb.INFO [2024-07-01 12:53:30.419][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-01 12:53:30.420][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:30.421][biodb::testThat]
biodb.DEBUG[2024-07-01 12:53:30.539][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-07-01 12:53:30.648][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:30.650][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:30.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:30.651][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:30.652][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:30.653][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:30.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:30.655][ef$get] fields variable is a list.
biodb.INFO [2024-07-01 12:53:30.657][biodb::testThat]
biodb.INFO [2024-07-01 12:53:30.658][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-07-01 12:53:30.659][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:30.660][biodb::testThat]
biodb.TRACE[2024-07-01 12:53:30.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:30.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:30.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:30.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:30.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:30.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:30.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:30.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:30.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:30.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:30.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:30.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:30.790][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:30.794][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:30.795][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-01 12:53:30.797][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:30.798][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-01 12:53:30.872][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:30.876][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:30.878][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-01 12:53:30.879][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:30.880][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-07-01 12:53:30.898][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-01 12:53:30.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-01 12:53:30.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:30.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:30.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:30.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:30.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:30.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:30.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:30.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:30.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:30.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:30.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:30.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:30.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:30.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:30.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:30.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:30.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:30.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:30.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:30.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:30.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:30.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:30.936][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:30.954][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:30.955][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:30.978][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:31.055][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:31.128][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:31.131][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-07-01 12:53:31.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-07-01 12:53:31.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:31.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:31.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:31.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:31.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:31.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:31.150][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[2024-07-01 12:53:31.151][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-07-01 12:53:31.198][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:31.200][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-07-01 12:53:31.201][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:31.202][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:31.203][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:31.204][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:31.205][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:31.206][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:31.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:31.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:31.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:31.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:31.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:31.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:31.219][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[2024-07-01 12:53:31.220][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-07-01 12:53:31.223][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:31.223][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:31.225][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-07-01 12:53:31.301][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-07-01 12:53:31.384][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:31.387][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-07-01 12:53:31.391][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-07-01 12:53:31.395][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-07-01 12:53:31.397][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:31.399][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:31.400][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:31.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:31.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:31.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:31.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:31.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:31.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:31.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:31.415][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:31.416][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:31.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.418][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:31.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:31.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.423][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:31.423][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:31.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.425][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.426][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:31.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:31.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.430][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:31.431][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:31.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.432][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.434][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:31.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:31.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.438][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:31.439][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:31.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.440][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:31.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:31.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.445][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:31.446][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:31.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.447][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:31.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:31.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.452][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:31.452][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:31.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.454][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.455][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:31.456][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.457][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.458][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:31.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.462][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:31.462][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:31.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.464][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:31.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:31.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.469][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:31.469][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:31.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.471][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:31.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:31.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.476][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:31.477][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:31.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.479][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.481][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:31.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:31.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.484][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:31.485][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:31.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.486][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.487][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:31.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:31.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:31.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:31.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:31.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:31.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:31.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:31.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:31.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:31.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:31.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:31.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:31.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:31.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:31.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:31.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:31.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:31.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:31.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:31.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:31.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:31.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:31.533][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-07-01 12:53:31.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:31.555][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:31.558][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:31.559][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:31.561][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:31.635][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:31.706][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:31.708][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-07-01 12:53:31.713][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-07-01 12:53:31.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:31.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:31.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:31.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:31.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:31.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:31.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:31.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:31.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:31.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:31.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:31.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:31.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:31.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:31.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:31.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:31.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:31.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:31.777][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-07-01 12:53:31.778][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:31.779][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-07-01 12:53:31.780][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:31.781][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:31.782][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:31.783][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:31.784][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:31.785][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:31.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:31.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:31.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:31.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:31.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:31.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:31.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:31.809][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-07-01 12:53:31.812][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:31.813][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-01 12:53:31.814][rule$waitAsNeeded] Wait 0.156441 second(s).
biodb.TRACE[2024-07-01 12:53:32.122][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-07-01 12:53:32.201][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-07-01 12:53:32.274][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:32.277][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-07-01 12:53:32.280][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-07-01 12:53:32.283][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-07-01 12:53:32.284][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:32.285][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:32.286][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:32.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:32.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:32.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:32.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:32.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:32.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:32.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:32.300][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.301][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.302][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.307][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:32.308][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:32.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.309][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.310][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:32.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:32.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.314][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:32.315][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:32.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.326][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.327][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:32.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:32.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.331][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:32.332][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:32.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.334][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:32.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:32.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.340][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:32.341][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:32.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.343][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:32.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:32.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.349][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:32.351][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:32.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.353][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.355][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:32.356][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.358][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.360][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:32.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.364][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:32.366][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:32.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.368][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:32.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:32.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.373][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:32.375][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:32.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.377][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:32.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:32.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.383][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:32.384][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:32.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.387][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.388][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:32.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:32.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.393][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:32.394][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:32.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.396][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.398][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:32.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:32.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:32.435][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-07-01 12:53:32.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:32.474][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:32.478][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:32.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-01 12:53:32.481][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:32.483][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-01 12:53:32.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:32.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:32.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:32.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:32.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:32.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:32.497][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[2024-07-01 12:53:32.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:32.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:32.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:32.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:32.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:32.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:32.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:32.518][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[2024-07-01 12:53:32.519][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-07-01 12:53:32.520][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:32.521][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-07-01 12:53:32.522][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:32.523][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:32.524][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:32.525][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:32.526][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:32.527][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:32.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:32.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:32.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:32.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:32.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:32.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:32.541][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[2024-07-01 12:53:32.542][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-07-01 12:53:32.545][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:32.546][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:32.547][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-07-01 12:53:32.623][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-07-01 12:53:32.693][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:32.696][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-07-01 12:53:32.700][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-07-01 12:53:32.702][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-07-01 12:53:32.704][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:32.705][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:32.716][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:32.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:32.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:32.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:32.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:32.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:32.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:32.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:32.730][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.731][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.733][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.737][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:32.738][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:32.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.740][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.741][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:32.742][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:32.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.744][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.745][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:32.746][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:32.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.748][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.749][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:32.749][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:32.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.751][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.752][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:32.753][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:32.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.755][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.756][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:32.757][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.758][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.759][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:32.760][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:32.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.762][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.763][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:32.764][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:32.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.765][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:32.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:32.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.770][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:32.771][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:32.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.772][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.774][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:32.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:32.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.777][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:32.778][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:32.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.779][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:32.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:32.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:32.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:32.822][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-07-01 12:53:32.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:32.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:32.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:32.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:32.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:32.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:32.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:32.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:32.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:32.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:32.852][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[2024-07-01 12:53:32.853][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-07-01 12:53:32.854][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:32.856][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-07-01 12:53:32.857][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:32.858][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:32.859][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:32.860][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:32.861][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:32.862][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:32.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:32.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:32.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:32.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:32.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:32.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:32.876][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[2024-07-01 12:53:32.877][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-07-01 12:53:32.880][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:32.881][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:32.883][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-07-01 12:53:32.964][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-07-01 12:53:33.045][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:33.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-07-01 12:53:33.051][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-07-01 12:53:33.055][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-07-01 12:53:33.056][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:33.058][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:33.059][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:33.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:33.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:33.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:33.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:33.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:33.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:33.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:33.073][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.074][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.076][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.081][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:33.082][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:33.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.083][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.084][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:33.085][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:33.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.088][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.089][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:33.090][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:33.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.092][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.093][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:33.101][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:33.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.106][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.107][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:33.108][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:33.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.110][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.111][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:33.112][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.114][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.115][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:33.116][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:33.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.118][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.119][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:33.120][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:33.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.121][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:33.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:33.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.127][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:33.127][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:33.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.129][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.130][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:33.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:33.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.133][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:33.134][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:33.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.136][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:33.170][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-07-01 12:53:33.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:33.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:33.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:33.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:33.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:33.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:33.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:33.198][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[2024-07-01 12:53:33.199][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-07-01 12:53:33.238][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:33.240][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-07-01 12:53:33.242][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:33.243][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:33.244][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:33.245][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:33.246][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:33.246][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:33.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:33.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:33.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:33.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:33.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:33.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:33.259][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[2024-07-01 12:53:33.260][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-07-01 12:53:33.264][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:33.265][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:33.266][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-07-01 12:53:33.342][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-07-01 12:53:33.415][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:33.418][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-07-01 12:53:33.422][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-07-01 12:53:33.425][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-07-01 12:53:33.426][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:33.428][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:33.429][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:33.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:33.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:33.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:33.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:33.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:33.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:33.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:33.444][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.445][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.446][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.451][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:33.452][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:33.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.454][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.455][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:33.456][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:33.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.458][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.459][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:33.460][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:33.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.462][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.463][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:33.464][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:33.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.465][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.467][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:33.468][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:33.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.470][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.471][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:33.472][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.473][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.474][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:33.475][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:33.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.477][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.478][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:33.479][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:33.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.480][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:33.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:33.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.486][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:33.487][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:33.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.488][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.490][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:33.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:33.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.493][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:33.494][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:33.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.496][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:33.540][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-07-01 12:53:33.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:33.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:33.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:33.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:33.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:33.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:33.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:33.566][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[2024-07-01 12:53:33.567][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-07-01 12:53:33.568][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:33.570][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-07-01 12:53:33.571][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:33.572][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:33.573][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:33.574][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:33.574][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:33.575][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:33.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:33.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:33.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:33.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:33.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:33.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:33.587][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[2024-07-01 12:53:33.589][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-07-01 12:53:33.592][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:33.592][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:33.594][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-07-01 12:53:33.687][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-07-01 12:53:33.761][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:33.764][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-07-01 12:53:33.768][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-07-01 12:53:33.771][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-07-01 12:53:33.773][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:33.785][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:33.787][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:33.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:33.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:33.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:33.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:33.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:33.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:33.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:33.802][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.803][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.804][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.809][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:33.810][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:33.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.812][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.813][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:33.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:33.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.817][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:33.817][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:33.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.819][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.820][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:33.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:33.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.825][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:33.826][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:33.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.828][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:33.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:33.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.835][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:33.836][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:33.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.837][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:33.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:33.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.842][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:33.842][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:33.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.844][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.845][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:33.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:33.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.848][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:33.849][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.851][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.852][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:33.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.855][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:33.856][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:33.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.858][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:33.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:33.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.862][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:33.863][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:33.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.865][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:33.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:33.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.869][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:33.870][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:33.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.872][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.873][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:33.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:33.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.876][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:33.877][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:33.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.879][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.880][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:33.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:33.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:33.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:33.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:33.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:33.926][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-07-01 12:53:33.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:33.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:33.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:33.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:33.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:33.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:33.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:33.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:33.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:33.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:33.947][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[2024-07-01 12:53:33.948][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-07-01 12:53:33.948][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:33.950][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-07-01 12:53:33.951][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:33.952][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:33.953][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:33.954][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:33.955][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:33.956][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:33.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:33.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:33.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:33.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:33.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:33.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:33.970][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[2024-07-01 12:53:33.971][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-07-01 12:53:33.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:33.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:33.976][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-07-01 12:53:34.061][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-07-01 12:53:34.137][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:34.140][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-07-01 12:53:34.144][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-07-01 12:53:34.147][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-07-01 12:53:34.149][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:34.150][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:34.151][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:34.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:34.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:34.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:34.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:34.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:34.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:34.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:34.176][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.178][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.180][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.185][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:34.186][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:34.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.187][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.189][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:34.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:34.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.192][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:34.193][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:34.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.195][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.196][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:34.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:34.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.200][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:34.201][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:34.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.202][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.203][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:34.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:34.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.207][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.208][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.210][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.211][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.215][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:34.216][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:34.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.217][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.218][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:34.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:34.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.222][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:34.223][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.224][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.225][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:34.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.229][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.230][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.231][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.236][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:34.237][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:34.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.238][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:34.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:34.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.243][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:34.244][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:34.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.245][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.247][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:34.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:34.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.250][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:34.251][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:34.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.252][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.253][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:34.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:34.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:34.299][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-07-01 12:53:34.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:34.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:34.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:34.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:34.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:34.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:34.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:34.320][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[2024-07-01 12:53:34.321][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-07-01 12:53:34.322][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:34.324][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-07-01 12:53:34.325][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:34.327][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:34.328][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:34.329][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:34.330][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:34.330][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:34.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:34.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:34.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:34.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:34.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:34.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:34.343][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[2024-07-01 12:53:34.344][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-07-01 12:53:34.347][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:34.348][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:34.350][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-07-01 12:53:34.428][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-07-01 12:53:34.499][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:34.502][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-07-01 12:53:34.506][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-07-01 12:53:34.509][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-07-01 12:53:34.511][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:34.512][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:34.513][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:34.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:34.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:34.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:34.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:34.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:34.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:34.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:34.528][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.529][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.531][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.535][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:34.536][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:34.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.538][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.539][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:34.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:34.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.553][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:34.553][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:34.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.555][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.556][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:34.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:34.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.560][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:34.561][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:34.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.562][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:34.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:34.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.567][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.568][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.569][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.574][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:34.575][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:34.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.576][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.578][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:34.578][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.580][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.581][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:34.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.584][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.585][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.587][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.591][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:34.592][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:34.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.593][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:34.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:34.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.598][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:34.599][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:34.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.600][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.601][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:34.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:34.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.605][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:34.606][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:34.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.607][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.608][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:34.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:34.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:34.651][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-07-01 12:53:34.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:34.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:34.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:34.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:34.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:34.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:34.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:34.671][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[2024-07-01 12:53:34.672][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-07-01 12:53:34.673][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:34.674][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-07-01 12:53:34.675][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:34.676][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:34.677][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:34.678][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:34.679][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:34.680][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:34.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:34.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:34.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:34.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:34.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:34.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:34.692][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[2024-07-01 12:53:34.694][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-07-01 12:53:34.697][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:34.697][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:34.699][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-07-01 12:53:34.779][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-07-01 12:53:34.851][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:34.853][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-07-01 12:53:34.857][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-07-01 12:53:34.860][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-07-01 12:53:34.861][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:34.862][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:34.863][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:34.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:34.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:34.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:34.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:34.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:34.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:34.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:34.877][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.878][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.879][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.884][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:34.885][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:34.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.886][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.887][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:34.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:34.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.891][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:34.892][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:34.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.893][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.894][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:34.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:34.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.898][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:34.899][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:34.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.900][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:34.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:34.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.916][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.917][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.918][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:34.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.923][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:34.924][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:34.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.925][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.927][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:34.928][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.929][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.930][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:34.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.934][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.935][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.936][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:34.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.941][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:34.942][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:34.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.943][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:34.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:34.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.948][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:34.949][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:34.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.951][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.952][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:34.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:34.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.955][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:34.956][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:34.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.957][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.958][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:34.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:34.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:34.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:34.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:34.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:34.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:34.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:34.996][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-07-01 12:53:34.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:34.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:35.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:35.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:35.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:35.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:35.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:35.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:35.025][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[2024-07-01 12:53:35.026][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-07-01 12:53:35.027][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:35.028][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-07-01 12:53:35.029][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:35.030][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:35.031][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:35.032][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:35.033][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:35.034][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:35.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:35.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:35.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:35.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:35.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:35.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:35.047][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[2024-07-01 12:53:35.048][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-07-01 12:53:35.051][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:35.052][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:35.053][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-07-01 12:53:35.129][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-07-01 12:53:35.201][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:35.204][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-07-01 12:53:35.207][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-07-01 12:53:35.210][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-07-01 12:53:35.211][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:35.212][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:35.213][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:35.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:35.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:35.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:35.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:35.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:35.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:35.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:35.227][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.228][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.229][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.234][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:35.234][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:35.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.236][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.237][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:35.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:35.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.240][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:35.241][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:35.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.243][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.244][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:35.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:35.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.247][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:35.248][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:35.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.249][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.250][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:35.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:35.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.253][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:35.254][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:35.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.256][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:35.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:35.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.260][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:35.261][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:35.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.262][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.263][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:35.274][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.276][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.278][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:35.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.281][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:35.282][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:35.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.283][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:35.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:35.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.287][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:35.288][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:35.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.290][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:35.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:35.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.294][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:35.295][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:35.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.296][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.297][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:35.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:35.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.301][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:35.301][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:35.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.303][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.304][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:35.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:35.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:35.338][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-07-01 12:53:35.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:35.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:35.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:35.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:35.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:35.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:35.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:35.358][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[2024-07-01 12:53:35.359][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-07-01 12:53:35.360][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:35.361][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-07-01 12:53:35.362][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:35.363][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:35.370][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:35.372][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:35.373][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:35.374][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:35.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:35.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:35.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:35.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:35.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:35.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:35.386][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[2024-07-01 12:53:35.387][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-07-01 12:53:35.390][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:35.391][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:35.392][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-07-01 12:53:35.465][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-07-01 12:53:35.538][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:35.540][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-07-01 12:53:35.544][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-07-01 12:53:35.546][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-07-01 12:53:35.548][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:35.549][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:35.550][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:35.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:35.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:35.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:35.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:35.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:35.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:35.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:35.562][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.563][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.565][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.569][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:35.570][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:35.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.572][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.573][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:35.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:35.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.576][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:35.577][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:35.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.578][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.579][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:35.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:35.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.582][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:35.583][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:35.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.585][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:35.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:35.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.589][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:35.590][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:35.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.591][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.592][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:35.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:35.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.595][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:35.596][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:35.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.597][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.599][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:35.599][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.601][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.602][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:35.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.605][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:35.606][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:35.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.607][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:35.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:35.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.618][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:35.622][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:35.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.624][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:35.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:35.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.629][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:35.630][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:35.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.631][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.632][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:35.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:35.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.635][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:35.636][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:35.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.638][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.639][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:35.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:35.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:35.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:35.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:35.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:35.673][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-07-01 12:53:35.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:35.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:35.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:35.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:35.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:35.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:35.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:35.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:35.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:35.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:35.692][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[2024-07-01 12:53:35.693][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-07-01 12:53:35.694][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:35.695][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-07-01 12:53:35.696][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:35.697][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:35.698][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:35.699][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:35.700][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:35.701][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:35.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:35.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:35.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:35.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:35.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:35.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:35.712][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[2024-07-01 12:53:35.719][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-07-01 12:53:35.723][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:35.723][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:35.725][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-07-01 12:53:35.884][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-07-01 12:53:35.980][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:35.982][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-07-01 12:53:35.986][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-07-01 12:53:35.988][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-07-01 12:53:35.990][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:35.991][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:35.992][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:35.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:35.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:35.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:36.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:36.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:36.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:36.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:36.006][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.007][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.009][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.013][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:36.014][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:36.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.015][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.017][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:36.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:36.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.020][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:36.021][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:36.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.022][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.023][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:36.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:36.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.026][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:36.027][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:36.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.029][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:36.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:36.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.033][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:36.034][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:36.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.035][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:36.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:36.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.039][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:36.040][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:36.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.042][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.043][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:36.044][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.045][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.046][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:36.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.050][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.050][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.052][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.056][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:36.057][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:36.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.058][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:36.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:36.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.063][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:36.064][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:36.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.065][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.066][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:36.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:36.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.079][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:36.081][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:36.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.082][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.083][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:36.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:36.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:36.118][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-07-01 12:53:36.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:36.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:36.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:36.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:36.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:36.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:36.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:36.137][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[2024-07-01 12:53:36.138][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-07-01 12:53:36.139][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:36.141][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-07-01 12:53:36.142][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:36.143][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:36.144][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:36.145][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:36.146][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:36.146][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:36.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:36.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:36.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:36.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:36.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:36.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:36.160][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[2024-07-01 12:53:36.161][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-07-01 12:53:36.165][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:36.166][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:36.167][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-07-01 12:53:36.264][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-07-01 12:53:36.351][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:36.354][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-07-01 12:53:36.358][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-07-01 12:53:36.370][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-07-01 12:53:36.372][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:36.374][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:36.375][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:36.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:36.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:36.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:36.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:36.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:36.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:36.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:36.388][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.389][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.391][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.395][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:36.396][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:36.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.398][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.399][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:36.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:36.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.402][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:36.403][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:36.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.404][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.405][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:36.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:36.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.408][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:36.409][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:36.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.411][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.412][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:36.413][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:36.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.414][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.415][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:36.416][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:36.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.417][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.418][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:36.419][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.421][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.422][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:36.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.425][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.427][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.429][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.434][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:36.435][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:36.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.436][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:36.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:36.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.441][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:36.442][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:36.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.444][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.445][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:36.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:36.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.448][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:36.449][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:36.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.451][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:36.496][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-07-01 12:53:36.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:36.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:36.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:36.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:36.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:36.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:36.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:36.516][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[2024-07-01 12:53:36.517][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-07-01 12:53:36.518][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:36.519][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-07-01 12:53:36.521][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:36.522][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:36.522][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:36.523][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:36.524][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:36.525][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:36.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:36.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:36.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:36.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:36.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:36.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:36.537][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[2024-07-01 12:53:36.539][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-07-01 12:53:36.542][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:36.542][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:36.544][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-07-01 12:53:36.731][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-07-01 12:53:36.806][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:36.808][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-07-01 12:53:36.812][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-07-01 12:53:36.814][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-07-01 12:53:36.815][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:36.816][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:36.817][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:36.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:36.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:36.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:36.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:36.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:36.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:36.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:36.830][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.831][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.833][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.837][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:36.848][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:36.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.851][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.853][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:36.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:36.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.856][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:36.857][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:36.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.859][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.860][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:36.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:36.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.863][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:36.864][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:36.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.866][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.867][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:36.868][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:36.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.870][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.871][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:36.871][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:36.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.873][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.874][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:36.875][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.877][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.878][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:36.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.882][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.883][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.884][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:36.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.890][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:36.891][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:36.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.893][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:36.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:36.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.898][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:36.899][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:36.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.900][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.901][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:36.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:36.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.905][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:36.906][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:36.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.908][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:36.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:36.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:36.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:36.944][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-07-01 12:53:36.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:36.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:36.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:36.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:36.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:36.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:36.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:36.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:36.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:36.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:36.973][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[2024-07-01 12:53:36.975][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-07-01 12:53:36.976][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:36.977][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.INFO [2024-07-01 12:53:36.978][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-07-01 12:53:36.980][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:36.981][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:36.982][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:36.983][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:36.984][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:36.985][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:36.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:36.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:36.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:36.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:36.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:36.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:36.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:37.000][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-07-01 12:53:37.003][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:37.004][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:37.005][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-07-01 12:53:37.087][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-07-01 12:53:37.223][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:37.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-07-01 12:53:37.226][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-07-01 12:53:37.228][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-07-01 12:53:37.229][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:37.229][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:37.230][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:37.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:37.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:37.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:37.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:37.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:37.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:37.235][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[2024-07-01 12:53:37.237][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.238][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.239][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.241][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:37.242][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:37.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.242][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.243][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:37.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:37.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.244][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:37.245][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:37.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.245][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.246][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:37.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:37.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.248][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:37.249][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:37.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.251][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:37.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:37.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.263][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.268][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.270][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.273][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:37.273][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:37.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.274][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.274][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:37.275][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.276][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.276][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:37.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.278][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.278][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.281][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.286][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:37.287][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:37.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.289][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.290][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:37.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:37.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.293][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:37.293][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:37.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.294][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.294][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:37.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:37.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.296][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:37.296][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:37.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.297][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:37.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:37.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:37.328][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-07-01 12:53:37.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:37.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:37.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:37.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:37.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:37.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:37.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:37.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:37.349][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-07-01 12:53:37.350][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:37.351][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-07-01 12:53:37.352][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:37.352][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:37.353][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:37.353][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:37.353][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:37.354][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:37.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:37.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:37.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:37.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:37.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:37.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:37.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:37.365][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-07-01 12:53:37.367][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:37.367][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:37.368][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-07-01 12:53:37.458][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-07-01 12:53:37.536][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:37.538][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-07-01 12:53:37.541][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-07-01 12:53:37.544][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-07-01 12:53:37.546][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:37.547][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:37.548][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:37.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:37.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:37.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:37.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:37.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:37.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:37.554][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[2024-07-01 12:53:37.556][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.556][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.557][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.559][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:37.559][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:37.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.560][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.560][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:37.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:37.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.562][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:37.562][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:37.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.563][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.564][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:37.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:37.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.565][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:37.566][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:37.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.567][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:37.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:37.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.569][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.569][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.570][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.572][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:37.573][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:37.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.575][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.577][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:37.592][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.594][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.596][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:37.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.597][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.598][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.599][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.601][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:37.601][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:37.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.602][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:37.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:37.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.604][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:37.605][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:37.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.606][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.606][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:37.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:37.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.609][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:37.610][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:37.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.612][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.613][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:37.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:37.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:37.633][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-07-01 12:53:37.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:37.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:37.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:37.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:37.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:37.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:37.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:37.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:37.644][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-07-01 12:53:37.645][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:37.647][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-07-01 12:53:37.648][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:37.655][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:37.657][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:37.658][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:37.660][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:37.661][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:37.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:37.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:37.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:37.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:37.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:37.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:37.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:37.675][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-07-01 12:53:37.677][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:37.678][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:37.680][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-07-01 12:53:37.828][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-07-01 12:53:37.896][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:37.897][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-07-01 12:53:37.899][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-07-01 12:53:37.901][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-07-01 12:53:37.901][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:37.902][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:37.902][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:37.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:37.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:37.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:37.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:37.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:37.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:37.908][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[2024-07-01 12:53:37.911][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.912][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.914][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:37.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:37.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.916][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:37.916][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:37.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.917][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.917][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:37.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:37.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.920][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:37.921][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:37.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.922][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.924][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:37.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:37.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.928][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:37.929][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:37.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.930][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.932][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:37.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:37.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.936][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.937][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.938][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:37.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.943][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:37.944][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:37.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.945][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.947][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:37.947][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.949][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.950][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:37.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:37.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.954][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.954][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.956][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:37.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.972][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:37.973][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:37.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.976][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.977][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:37.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:37.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.981][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:37.982][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:37.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.983][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.984][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:37.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:37.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.988][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:37.989][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:37.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.991][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.992][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:37.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:37.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:37.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:37.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:37.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:38.029][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-07-01 12:53:38.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:38.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:38.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:38.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:38.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:38.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:38.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:38.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:38.041][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-07-01 12:53:38.042][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:38.043][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-07-01 12:53:38.043][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:38.044][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:38.044][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:38.044][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:38.045][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:38.046][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:38.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:38.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:38.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:38.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:38.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:38.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:38.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:38.067][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-07-01 12:53:38.071][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:38.072][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:38.073][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-07-01 12:53:38.219][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-07-01 12:53:38.318][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:38.321][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-07-01 12:53:38.328][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-07-01 12:53:38.331][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-07-01 12:53:38.333][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:38.334][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:38.335][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:38.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:38.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:38.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:38.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:38.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:38.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:38.346][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.TRACE[2024-07-01 12:53:38.348][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.349][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.351][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.355][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:38.356][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:38.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.358][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.359][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:38.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:38.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.362][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:38.363][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:38.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.364][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.365][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:38.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:38.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.369][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:38.370][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:38.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.371][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:38.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:38.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.376][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:38.376][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:38.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.378][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:38.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:38.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.382][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:38.383][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:38.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.385][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.386][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:38.387][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.388][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.389][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:38.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.393][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:38.394][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:38.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.395][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:38.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:38.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.400][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:38.401][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:38.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.402][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:38.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:38.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.407][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:38.408][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:38.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.410][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.411][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:38.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:38.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.425][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:38.426][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:38.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.428][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.429][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:38.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:38.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:38.466][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-07-01 12:53:38.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:38.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:38.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:38.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:38.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:38.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:38.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:38.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:38.488][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-07-01 12:53:38.489][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:38.490][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-07-01 12:53:38.491][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:38.492][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:38.493][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:38.494][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:38.495][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:38.496][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:38.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:38.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:38.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:38.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:38.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:38.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:38.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:38.510][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-07-01 12:53:38.513][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:38.514][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:38.515][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-07-01 12:53:38.702][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-07-01 12:53:38.866][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:38.868][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-07-01 12:53:38.878][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-07-01 12:53:38.886][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-07-01 12:53:38.888][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:38.889][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:38.890][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:38.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:38.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:38.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:38.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:38.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:38.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:38.902][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.TRACE[2024-07-01 12:53:38.904][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.905][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.907][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.912][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:38.913][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:38.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.914][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.915][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:38.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:38.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.919][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:38.920][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:38.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.921][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.922][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:38.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:38.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.926][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:38.927][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:38.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.929][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:38.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:38.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.933][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:38.934][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:38.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.936][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:38.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:38.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.940][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:38.941][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:38.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.943][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.944][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:38.945][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.946][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.947][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:38.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:38.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.951][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:38.952][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:38.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.953][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:38.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:38.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.958][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:38.958][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:38.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.960][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:38.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:38.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.965][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:38.965][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:38.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.967][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.968][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:38.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:38.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.971][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:38.972][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:38.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.974][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.975][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:38.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:38.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:38.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:38.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:38.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:38.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:38.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:39.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:39.033][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-07-01 12:53:39.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:39.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:39.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:39.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:39.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:39.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:39.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:39.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:39.063][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-07-01 12:53:39.064][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:39.066][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.INFO [2024-07-01 12:53:39.067][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-07-01 12:53:39.068][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:39.069][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:39.070][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:39.071][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:39.072][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:39.073][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:39.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:39.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:39.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:39.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:39.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:39.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:39.086][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[2024-07-01 12:53:39.087][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-07-01 12:53:39.090][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:39.091][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:39.093][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-07-01 12:53:39.275][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-07-01 12:53:39.417][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:39.419][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-07-01 12:53:39.423][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-07-01 12:53:39.425][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-07-01 12:53:39.427][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:39.428][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:39.429][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:39.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:39.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:39.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:39.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:39.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:39.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:39.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:39.454][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.455][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.457][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.462][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:39.463][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:39.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.464][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.465][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:39.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:39.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.469][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:39.470][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:39.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.471][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:39.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:39.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.476][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:39.477][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:39.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.479][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:39.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:39.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.483][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:39.484][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:39.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.485][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:39.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:39.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.490][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:39.490][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:39.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.492][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.493][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:39.494][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.495][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.496][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:39.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.500][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:39.500][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:39.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.502][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:39.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:39.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.506][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:39.507][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:39.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.508][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:39.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:39.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.513][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:39.514][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:39.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.515][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.516][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:39.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:39.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.519][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:39.520][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:39.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.522][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.523][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:39.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:39.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:39.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:39.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:39.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:39.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:39.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:39.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:39.567][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-07-01 12:53:39.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:39.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:39.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:39.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:39.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:39.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:39.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:39.587][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[2024-07-01 12:53:39.588][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-07-01 12:53:39.589][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:39.590][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-07-01 12:53:39.591][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:39.592][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:39.593][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:39.594][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:39.595][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:39.596][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:39.598][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:39.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:39.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:39.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:39.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:39.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:39.608][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[2024-07-01 12:53:39.609][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-07-01 12:53:39.612][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:39.613][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:39.614][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-07-01 12:53:39.792][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-07-01 12:53:39.878][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:39.881][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-07-01 12:53:39.884][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-07-01 12:53:39.887][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-07-01 12:53:39.889][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:39.891][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:39.892][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:39.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:39.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:39.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:39.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:39.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:39.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:39.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:39.907][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.908][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.909][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:39.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:39.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.925][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:39.927][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:39.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.929][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.931][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:39.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:39.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.934][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:39.935][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:39.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.937][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.938][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:39.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:39.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.942][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:39.943][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:39.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.944][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.946][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:39.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:39.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.949][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:39.950][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:39.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.952][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:39.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:39.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.956][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:39.957][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:39.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.959][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.960][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:39.961][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.963][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.964][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:39.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:39.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.967][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:39.968][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:39.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.970][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:39.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:39.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.975][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:39.976][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:39.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.978][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:39.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:39.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.983][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:39.984][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:39.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.985][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.986][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:39.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:39.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.990][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:39.991][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:39.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.992][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.993][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:39.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:39.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:39.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:39.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:39.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:39.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:40.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:40.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:40.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:40.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:40.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:40.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:40.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:40.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:40.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:40.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:40.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:40.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:40.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:40.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:40.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:40.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:40.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:40.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.042][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-07-01 12:53:40.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.072][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:40.075][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:40.076][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:40.078][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:40.309][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:40.558][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:40.560][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-07-01 12:53:40.562][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-07-01 12:53:40.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.716][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.800][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:40.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:40.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:40.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:40.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:40.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:40.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:40.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:40.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:40.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:40.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:40.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:40.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:40.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:40.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:40.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:40.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:40.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:40.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:40.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:40.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:40.936][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:40.938][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:40.938][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:40.939][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:41.009][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:41.077][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:41.078][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-07-01 12:53:41.080][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-07-01 12:53:41.083][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:41.084][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:41.085][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:41.086][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:41.155][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:41.218][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:41.220][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-07-01 12:53:41.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-07-01 12:53:41.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:41.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:41.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:41.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:41.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:41.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:41.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:41.237][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-07-01 12:53:41.238][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:41.239][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-07-01 12:53:41.240][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:41.241][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:41.242][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:41.243][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:41.243][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:41.258][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:41.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:41.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:41.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:41.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:41.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:41.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:41.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:41.275][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-07-01 12:53:41.278][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:41.279][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:41.280][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-07-01 12:53:41.361][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-07-01 12:53:41.436][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:41.438][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-07-01 12:53:41.442][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-07-01 12:53:41.445][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-07-01 12:53:41.446][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:41.447][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:41.448][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:41.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:41.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:41.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:41.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:41.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:41.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:41.459][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.TRACE[2024-07-01 12:53:41.462][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:41.463][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:41.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.464][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:41.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:41.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.469][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:41.470][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:41.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.471][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.473][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:41.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:41.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.476][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:41.477][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:41.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.479][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:41.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:41.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.483][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:41.484][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:41.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.486][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:41.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:41.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.490][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:41.491][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:41.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.493][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:41.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:41.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.497][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:41.498][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:41.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.499][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.500][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:41.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:41.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.504][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:41.505][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:41.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.506][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.507][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:41.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:41.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.510][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.511][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.513][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.529][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:41.530][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:41.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.531][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:41.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:41.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.536][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:41.537][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:41.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.538][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.539][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:41.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:41.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.543][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:41.544][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:41.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.545][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.546][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:41.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:41.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:41.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:41.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:41.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:41.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:41.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:41.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:41.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:41.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:41.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:41.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:41.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:41.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:41.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:41.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:41.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:41.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:41.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:41.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:41.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:41.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:41.582][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-07-01 12:53:41.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:41.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:41.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:41.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:41.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:41.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:41.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:41.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:41.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:41.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:41.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:41.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:41.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:41.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:41.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:41.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:41.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:41.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:41.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:41.631][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-07-01 12:53:41.631][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:41.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-07-01 12:53:41.634][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:41.635][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:41.636][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:41.637][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:41.638][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:41.639][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:41.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:41.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:41.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:41.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:41.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:41.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:41.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:41.653][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-07-01 12:53:41.656][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:41.657][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-01 12:53:41.658][rule$waitAsNeeded] Wait 0.281217 second(s).
biodb.TRACE[2024-07-01 12:53:42.091][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-07-01 12:53:42.181][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-07-01 12:53:42.264][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:42.267][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-07-01 12:53:42.271][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-07-01 12:53:42.274][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-07-01 12:53:42.276][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:42.277][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:42.278][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:42.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:42.293][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:42.294][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:42.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.295][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:42.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:42.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.300][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:42.301][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:42.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.303][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.304][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:42.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:42.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.308][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:42.309][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:42.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.310][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.311][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:42.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:42.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.315][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:42.316][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:42.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.317][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.318][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:42.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:42.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.322][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:42.323][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:42.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.324][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:42.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:42.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.329][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:42.330][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:42.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.331][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.343][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:42.345][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:42.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.347][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.349][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:42.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:42.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.352][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.353][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.355][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.359][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:42.360][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:42.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.362][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.363][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:42.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:42.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.366][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:42.367][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:42.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.369][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.370][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:42.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:42.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.373][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:42.374][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:42.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.376][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.377][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:42.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:42.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:42.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:42.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:42.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:42.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:42.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:42.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:42.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:42.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:42.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:42.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:42.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:42.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:42.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:42.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:42.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:42.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:42.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:42.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:42.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:42.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.415][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-07-01 12:53:42.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.455][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:42.459][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:42.460][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-01 12:53:42.462][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:42.463][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-01 12:53:42.467][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.477][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.TRACE[2024-07-01 12:53:42.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.498][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.TRACE[2024-07-01 12:53:42.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.526][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[2024-07-01 12:53:42.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.555][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[2024-07-01 12:53:42.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.802][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[2024-07-01 12:53:42.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.823][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[2024-07-01 12:53:42.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.843][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.TRACE[2024-07-01 12:53:42.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.863][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.TRACE[2024-07-01 12:53:42.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.883][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.TRACE[2024-07-01 12:53:42.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.905][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.TRACE[2024-07-01 12:53:42.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.930][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[2024-07-01 12:53:42.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.953][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[2024-07-01 12:53:42.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.976][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[2024-07-01 12:53:42.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:42.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:42.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:42.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:42.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:42.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:42.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:42.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:42.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:42.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:42.999][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[2024-07-01 12:53:43.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.022][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[2024-07-01 12:53:43.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.045][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[2024-07-01 12:53:43.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.069][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[2024-07-01 12:53:43.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.092][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.093][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[2024-07-01 12:53:43.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.119][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[2024-07-01 12:53:43.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.152][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[2024-07-01 12:53:43.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.184][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:43.188][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:43.189][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-01 12:53:43.191][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:43.192][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-01 12:53:43.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.205][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[2024-07-01 12:53:43.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.225][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[2024-07-01 12:53:43.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.252][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[2024-07-01 12:53:43.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.278][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[2024-07-01 12:53:43.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.305][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[2024-07-01 12:53:43.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.326][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[2024-07-01 12:53:43.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.346][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.TRACE[2024-07-01 12:53:43.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.367][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[2024-07-01 12:53:43.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.389][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[2024-07-01 12:53:43.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.407][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.410][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[2024-07-01 12:53:43.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.431][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[2024-07-01 12:53:43.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.451][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[2024-07-01 12:53:43.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.478][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[2024-07-01 12:53:43.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.498][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.TRACE[2024-07-01 12:53:43.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.518][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[2024-07-01 12:53:43.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.538][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[2024-07-01 12:53:43.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.558][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[2024-07-01 12:53:43.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.579][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[2024-07-01 12:53:43.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.601][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.TRACE[2024-07-01 12:53:43.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.621][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[2024-07-01 12:53:43.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:43.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.648][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-01 12:53:43.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-01 12:53:43.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-01 12:53:43.660][biodb::testThat]
biodb.INFO [2024-07-01 12:53:43.661][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-07-01 12:53:43.662][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:43.663][biodb::testThat]
biodb.TRACE[2024-07-01 12:53:43.666][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-01 12:53:43.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-01 12:53:43.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.697][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[2024-07-01 12:53:43.700][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:43.704][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:43.705][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:43.707][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:43.787][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:43.863][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:43.865][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-07-01 12:53:43.870][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-07-01 12:53:43.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:43.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:43.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:43.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:43.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:43.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:43.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:43.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:43.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:43.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:43.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:43.895][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:43.899][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:43.900][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:43.902][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:43.979][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:44.053][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:44.056][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-07-01 12:53:44.061][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-07-01 12:53:44.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:44.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:44.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:44.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:44.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:44.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:44.075][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[2024-07-01 12:53:44.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:44.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:44.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:44.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:44.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:44.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:44.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:44.096][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[2024-07-01 12:53:44.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:44.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:44.108][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-01 12:53:44.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:44.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:44.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:44.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:44.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:44.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:44.131][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[2024-07-01 12:53:44.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.139][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.140][private$selectFields]
biodb.TRACE[2024-07-01 12:53:44.140][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:44.142][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:44.143][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.144][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.145][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.147][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.148][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.149][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.150][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.151][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.152][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.153][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.154][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.155][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.156][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:44.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.177][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-01 12:53:44.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:44.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:44.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:44.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:44.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:44.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:44.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:44.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.196][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.197][private$selectFields]
biodb.TRACE[2024-07-01 12:53:44.197][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:44.198][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:44.199][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.200][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.201][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.202][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.203][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.204][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.205][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.206][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.207][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.208][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.209][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.210][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.211][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:44.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.222][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-01 12:53:44.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:44.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:44.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:44.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:44.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:44.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:44.234][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[2024-07-01 12:53:44.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.242][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.243][private$selectFields]
biodb.TRACE[2024-07-01 12:53:44.244][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:44.245][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:44.245][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.246][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.247][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.249][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.250][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.250][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.252][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.253][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.254][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:44.254][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.255][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.257][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.258][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:44.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:44.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.269][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-01 12:53:44.270][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-01 12:53:44.270][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-01 12:53:44.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:44.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:44.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:44.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:44.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:44.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:44.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:44.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:44.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:44.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:44.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:44.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:44.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:44.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:44.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:44.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:44.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:44.360][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[2024-07-01 12:53:44.363][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:44.367][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:44.368][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:44.370][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:44.445][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:44.518][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:44.521][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-07-01 12:53:44.525][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-07-01 12:53:44.530][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:44.533][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:44.534][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-01 12:53:44.535][rule$waitAsNeeded] Wait 0.170921 second(s).
biodb.TRACE[2024-07-01 12:53:44.858][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:44.931][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:45.005][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:45.007][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-07-01 12:53:45.012][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-07-01 12:53:45.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.115][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-01 12:53:45.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.155][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.156][private$selectFields]
biodb.TRACE[2024-07-01 12:53:45.157][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:45.157][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:45.158][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.159][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.160][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.162][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.162][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.163][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.165][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.166][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.166][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.167][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.168][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.170][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.170][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:45.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.181][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-01 12:53:45.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.191][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[2024-07-01 12:53:45.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.233][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.235][private$selectFields]
biodb.TRACE[2024-07-01 12:53:45.235][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:45.236][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:45.237][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.238][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.239][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.240][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.241][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.242][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.244][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.244][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.255][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.256][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.257][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.259][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.260][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:45.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.271][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-01 12:53:45.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.290][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.291][private$selectFields]
biodb.TRACE[2024-07-01 12:53:45.292][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:45.292][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:45.293][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.294][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.295][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.296][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.297][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.298][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.300][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.301][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.301][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.302][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.303][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.305][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.306][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:45.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.318][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-01 12:53:45.319][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-01 12:53:45.320][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-01 12:53:45.329][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-01 12:53:45.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-01 12:53:45.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-01 12:53:45.337][biodb::testThat]
biodb.INFO [2024-07-01 12:53:45.338][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-07-01 12:53:45.339][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:45.340][biodb::testThat]
biodb.TRACE[2024-07-01 12:53:45.343][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-01 12:53:45.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-01 12:53:45.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:45.381][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:45.385][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:45.386][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-01 12:53:45.387][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:45.388][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-01 12:53:45.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.412][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:45.415][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:45.417][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-01 12:53:45.418][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:45.419][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-01 12:53:45.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.463][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-01 12:53:45.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.483][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.484][private$selectFields]
biodb.TRACE[2024-07-01 12:53:45.485][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:45.486][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:45.487][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.488][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.489][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.491][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.492][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.493][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.494][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.495][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.496][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.496][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.497][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.499][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.500][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:45.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.511][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-01 12:53:45.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.521][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[2024-07-01 12:53:45.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.529][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.530][private$selectFields]
biodb.TRACE[2024-07-01 12:53:45.530][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:45.531][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:45.532][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.533][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.534][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.535][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.536][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.537][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.538][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.539][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.540][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.540][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.541][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.543][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.544][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:45.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.554][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-01 12:53:45.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.572][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.573][private$selectFields]
biodb.TRACE[2024-07-01 12:53:45.574][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:45.574][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:45.575][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.576][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.577][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.578][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.579][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.580][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.581][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.582][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.583][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.584][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.585][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.586][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.587][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:45.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.598][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-01 12:53:45.598][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-01 12:53:45.599][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-01 12:53:45.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:45.636][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:45.640][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:45.641][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-07-01 12:53:45.642][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:45.643][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-07-01 12:53:45.647][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:45.650][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:45.651][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-07-01 12:53:45.652][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:45.653][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-07-01 12:53:45.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:45.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.726][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-01 12:53:45.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.746][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.747][private$selectFields]
biodb.TRACE[2024-07-01 12:53:45.748][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:45.749][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:45.749][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.750][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.751][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.753][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.753][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.754][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.756][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.757][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.757][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.758][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.759][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.761][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.761][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:45.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.772][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-01 12:53:45.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.783][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[2024-07-01 12:53:45.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.791][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.791][private$selectFields]
biodb.TRACE[2024-07-01 12:53:45.792][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:45.793][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:45.794][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.795][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.795][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.797][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.798][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.799][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.800][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.801][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.802][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.803][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.804][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.805][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.806][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:45.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.817][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-01 12:53:45.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.835][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.836][private$selectFields]
biodb.TRACE[2024-07-01 12:53:45.837][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:45.838][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:45.838][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.839][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.840][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.842][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.842][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.843][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.845][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.846][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.846][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:45.847][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.848][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.850][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.850][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:45.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:45.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.861][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-01 12:53:45.862][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-01 12:53:45.863][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-01 12:53:45.872][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-01 12:53:45.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-01 12:53:45.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-01 12:53:45.881][biodb::testThat]
biodb.INFO [2024-07-01 12:53:45.882][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-07-01 12:53:45.883][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:45.884][biodb::testThat]
biodb.TRACE[2024-07-01 12:53:45.887][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-01 12:53:45.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-01 12:53:45.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:45.924][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:45.927][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:45.929][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-01 12:53:45.930][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:45.931][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-01 12:53:45.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.956][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:45.960][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:45.961][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-01 12:53:45.962][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:45.964][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-01 12:53:45.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:45.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:45.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:45.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:45.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:45.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:45.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:45.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:45.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:45.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:45.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:45.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:46.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:46.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:46.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:46.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:46.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:46.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:46.009][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-01 12:53:46.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:46.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.035][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.036][private$selectFields]
biodb.TRACE[2024-07-01 12:53:46.037][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:46.038][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:46.038][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.039][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.040][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.041][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.042][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.043][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.045][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.046][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.046][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.047][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.048][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.049][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.050][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:46.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.061][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-01 12:53:46.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.071][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[2024-07-01 12:53:46.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.079][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.080][private$selectFields]
biodb.TRACE[2024-07-01 12:53:46.081][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:46.081][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:46.082][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.083][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.084][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.085][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.086][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.087][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.088][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.089][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.090][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.090][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.091][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.093][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.094][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:46.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.104][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-01 12:53:46.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:46.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.122][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.123][private$selectFields]
biodb.TRACE[2024-07-01 12:53:46.124][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:46.124][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:46.125][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.126][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.127][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.129][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.129][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.130][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.132][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.133][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.133][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.134][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.135][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.136][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.137][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:46.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.148][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-01 12:53:46.149][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-01 12:53:46.149][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-01 12:53:46.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:46.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:46.196][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:46.200][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:46.201][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-07-01 12:53:46.202][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:46.203][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-07-01 12:53:46.206][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:46.209][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:46.210][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-07-01 12:53:46.211][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:46.213][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-07-01 12:53:46.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:46.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:46.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:46.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:46.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:46.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:46.274][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-01 12:53:46.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:46.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.293][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.294][private$selectFields]
biodb.TRACE[2024-07-01 12:53:46.295][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:46.295][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:46.296][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.297][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.298][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.299][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.300][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.303][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.303][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.304][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.305][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.306][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.307][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.308][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:46.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.319][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-01 12:53:46.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.336][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[2024-07-01 12:53:46.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.343][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.344][private$selectFields]
biodb.TRACE[2024-07-01 12:53:46.345][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:46.345][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:46.346][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.347][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.348][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.349][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.350][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.351][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.352][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.353][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.354][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.355][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.355][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.357][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.358][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:46.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.368][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-01 12:53:46.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-01 12:53:46.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.386][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.387][private$selectFields]
biodb.TRACE[2024-07-01 12:53:46.388][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-01 12:53:46.389][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-01 12:53:46.390][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.391][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.392][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.393][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.394][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.395][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.396][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.397][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.398][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-01 12:53:46.399][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.400][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.401][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.402][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-01 12:53:46.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.412][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-01 12:53:46.413][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-01 12:53:46.414][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-01 12:53:46.434][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-01 12:53:46.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-01 12:53:46.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-01 12:53:46.442][biodb::testThat]
biodb.INFO [2024-07-01 12:53:46.443][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-07-01 12:53:46.444][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:46.445][biodb::testThat]
biodb.DEBUG[2024-07-01 12:53:46.446][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-07-01 12:53:46.447][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:46.449][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-07-01 12:53:46.450][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:46.451][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:46.452][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:46.453][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:46.454][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:46.454][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:46.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:46.468][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-07-01 12:53:46.471][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:46.472][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:46.474][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-07-01 12:53:46.546][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-07-01 12:53:46.617][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:46.619][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-07-01 12:53:46.623][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-07-01 12:53:46.626][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-07-01 12:53:46.627][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:46.628][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:46.629][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:46.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.642][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[2024-07-01 12:53:46.645][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:46.646][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:46.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.648][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:46.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:46.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.653][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:46.654][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:46.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.656][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.657][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:46.659][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:46.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.661][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.662][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:46.663][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:46.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.665][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.667][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:46.668][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:46.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.669][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.670][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:46.671][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:46.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.673][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.674][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:46.675][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:46.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.677][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.678][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.679][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:46.679][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.680][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.681][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:46.682][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:46.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.684][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.685][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:46.686][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:46.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.687][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.688][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:46.689][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:46.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.691][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:46.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:46.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:46.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:46.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:46.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:46.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:46.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:46.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:46.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:46.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:46.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:46.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:46.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:46.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:46.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:46.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:46.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:46.724][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-07-01 12:53:46.725][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-07-01 12:53:46.734][biodb::testThat]
biodb.INFO [2024-07-01 12:53:46.735][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-07-01 12:53:46.736][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:46.737][biodb::testThat]
biodb.DEBUG[2024-07-01 12:53:46.748][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-07-01 12:53:46.750][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-07-01 12:53:46.751][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-07-01 12:53:46.752][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-07-01 12:53:46.753][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-07-01 12:53:46.754][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:46.755][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:46.756][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:46.757][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:46.758][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:46.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.772][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[2024-07-01 12:53:46.773][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-07-01 12:53:46.776][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:46.777][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:46.779][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-07-01 12:53:46.854][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-07-01 12:53:46.926][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:46.928][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-07-01 12:53:46.932][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-07-01 12:53:46.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:46.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:46.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:46.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:46.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:46.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:46.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:46.958][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-07-01 12:53:46.961][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:46.962][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:46.964][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-07-01 12:53:47.042][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-07-01 12:53:47.117][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:47.120][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-07-01 12:53:47.124][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-07-01 12:53:47.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:47.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:47.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:47.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:47.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:47.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:47.135][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[2024-07-01 12:53:47.137][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-07-01 12:53:47.139][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:47.140][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-01 12:53:47.142][rule$waitAsNeeded] Wait 0.332034 second(s).
biodb.TRACE[2024-07-01 12:53:47.622][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-07-01 12:53:47.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-07-01 12:53:47.762][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:47.764][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-07-01 12:53:47.766][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-07-01 12:53:47.767][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-07-01 12:53:47.769][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:47.770][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-07-01 12:53:47.770][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:47.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:47.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:47.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:47.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:47.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:47.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:47.779][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[2024-07-01 12:53:47.781][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.782][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.782][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.786][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:47.786][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:47.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.787][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.787][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:47.788][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:47.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.788][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.789][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:47.789][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:47.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.789][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.790][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:47.790][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:47.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.791][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.791][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:47.792][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:47.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.792][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.793][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:47.793][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:47.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.794][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.795][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:47.795][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:47.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.796][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.796][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:47.796][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:47.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.797][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.797][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:47.798][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:47.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.798][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.799][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:47.799][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:47.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.800][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:47.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:47.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:47.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:47.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:47.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:47.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:47.822][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[2024-07-01 12:53:47.824][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.825][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.827][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.831][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:47.832][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:47.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.834][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.835][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:47.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:47.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.837][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:47.837][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:47.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.838][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.838][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:47.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:47.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.840][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:47.840][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:47.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.841][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.842][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:47.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:47.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.843][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:47.843][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:47.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.845][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:47.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:47.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.850][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:47.851][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:47.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.853][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.854][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:47.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:47.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.857][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:47.858][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:47.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.860][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:47.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:47.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.864][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:47.865][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:47.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.865][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:47.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:47.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.867][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:47.868][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:47.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.868][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:47.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:47.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.870][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:47.871][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:47.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.872][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.872][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:47.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:47.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.873][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:47.874][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:47.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.874][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.875][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:47.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:47.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:47.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:47.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:47.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:47.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:47.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:47.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:47.903][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[2024-07-01 12:53:47.906][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.907][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.908][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.913][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:47.914][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:47.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.915][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.916][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:47.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:47.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.919][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:47.920][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:47.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.922][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.923][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:47.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:47.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.926][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:47.927][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:47.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.928][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:47.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:47.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.933][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:47.934][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:47.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.934][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:47.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:47.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.937][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:47.937][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:47.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.938][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.939][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:47.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:47.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.940][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:47.941][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:47.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.941][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.942][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:47.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:47.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.953][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:47.953][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:47.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.954][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:47.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:47.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.956][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:47.956][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:47.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.957][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:47.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:47.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.959][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:47.960][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:47.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.960][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.961][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:47.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:47.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.963][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:47.963][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:47.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.964][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.964][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:47.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:47.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:47.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:47.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:47.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:47.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:47.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:47.999][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-07-01 12:53:47.999][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-07-01 12:53:48.000][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-07-01 12:53:48.007][biodb::testThat]
biodb.INFO [2024-07-01 12:53:48.007][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-07-01 12:53:48.008][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:48.008][biodb::testThat]
biodb.INFO [2024-07-01 12:53:48.028][biodb::testThat]
biodb.INFO [2024-07-01 12:53:48.029][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-07-01 12:53:48.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:48.030][biodb::testThat]
biodb.INFO [2024-07-01 12:53:48.036][biodb::testThat]
biodb.INFO [2024-07-01 12:53:48.037][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-07-01 12:53:48.038][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:48.039][biodb::testThat]
biodb.DEBUG[2024-07-01 12:53:48.041][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:48.043][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:48.043][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:48.044][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:48.193][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:48.346][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:48.347][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-07-01 12:53:48.352][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-07-01 12:53:48.361][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:48.361][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:48.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:48.362][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:48.362][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:48.363][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:48.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:48.364][ef$get] fields variable is a list.
biodb.INFO [2024-07-01 12:53:48.365][biodb::testThat]
biodb.INFO [2024-07-01 12:53:48.365][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-07-01 12:53:48.365][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:48.366][biodb::testThat]
biodb.ERROR[2024-07-01 12:53:48.375][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-07-01 12:53:48.391][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-07-01 12:53:48.402][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-01 12:53:48.403][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-01 12:53:48.404][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-01 12:53:48.405][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-01 12:53:48.405][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.406][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.407][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-01 12:53:48.412][biodb::testContext]
biodb.INFO [2024-07-01 12:53:48.413][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-01 12:53:48.413][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-07-01 12:53:48.414][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-01 12:53:48.415][biodb::testContext]
biodb.INFO [2024-07-01 12:53:48.418][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-01 12:53:48.419][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-01 12:53:48.421][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:48.422][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-01 12:53:48.422][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-01 12:53:48.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.423][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[2024-07-01 12:53:48.423][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-01 12:53:48.424][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-01 12:53:48.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:48.425][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-01 12:53:48.425][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-01 12:53:48.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.426][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[2024-07-01 12:53:48.427][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-01 12:53:48.428][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-01 12:53:48.429][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-01 12:53:48.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:48.432][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-01 12:53:48.433][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-01 12:53:48.434][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-01 12:53:48.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.436][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[2024-07-01 12:53:48.436][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-01 12:53:48.436][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-01 12:53:48.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:48.438][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-01 12:53:48.438][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-01 12:53:48.438][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-01 12:53:48.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.441][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[2024-07-01 12:53:48.442][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-01 12:53:48.443][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-01 12:53:48.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:48.446][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-01 12:53:48.446][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-01 12:53:48.447][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-01 12:53:48.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.449][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[2024-07-01 12:53:48.450][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-01 12:53:48.451][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-01 12:53:48.452][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-01 12:53:48.453][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-01 12:53:48.454][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-01 12:53:48.454][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-01 12:53:48.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:48.457][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-01 12:53:48.457][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-01 12:53:48.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.458][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[2024-07-01 12:53:48.459][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-01 12:53:48.459][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-01 12:53:48.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:48.461][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-01 12:53:48.461][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-01 12:53:48.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.462][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[2024-07-01 12:53:48.470][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-01 12:53:48.471][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-01 12:53:48.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:48.472][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-01 12:53:48.472][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-01 12:53:48.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.473][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[2024-07-01 12:53:48.473][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-01 12:53:48.474][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-01 12:53:48.483][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-01 12:53:48.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:48.485][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-01 12:53:48.485][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-01 12:53:48.485][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-01 12:53:48.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.486][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[2024-07-01 12:53:48.487][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-01 12:53:48.488][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.488][self$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[2024-07-01 12:53:48.488][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.489][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:48.489][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.489][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.490][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.490][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.490][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-01 12:53:48.491][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:48.491][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.491][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-01 12:53:48.492][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:48.492][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.492][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.493][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:48.493][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:48.493][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:48.493][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-01 12:53:48.493][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-01 12:53:48.493][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:48.493][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:48.493][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:48.494][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:48.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:48.494][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:48.495][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.495][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.495][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:48.495][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:48.496][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.496][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.497][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-01 12:53:48.498][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.498][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-01 12:53:48.498][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.499][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:48.499][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.500][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.500][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.500][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.501][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-01 12:53:48.501][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:48.501][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.502][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-01 12:53:48.502][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:48.502][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.503][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.503][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:48.503][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:48.503][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:48.503][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-01 12:53:48.503][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-01 12:53:48.503][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:48.504][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:48.504][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:48.504][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:48.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:48.505][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:48.505][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.506][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.506][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:48.506][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:48.507][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.507][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.507][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-01 12:53:48.508][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.509][self$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[2024-07-01 12:53:48.509][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.509][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:48.510][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.510][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.510][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.511][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.511][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-01 12:53:48.511][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:48.512][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.512][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-01 12:53:48.513][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:48.513][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.513][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.514][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.514][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:48.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:48.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:48.515][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:48.515][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:48.516][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:48.516][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.516][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.517][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:48.517][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:48.517][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.518][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.519][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-01 12:53:48.521][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.521][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-01 12:53:48.521][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.522][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:48.523][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.523][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.523][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.524][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.524][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-01 12:53:48.525][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:48.525][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.526][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-01 12:53:48.526][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:48.526][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.527][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.527][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.527][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:48.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:48.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:48.528][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:48.529][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:48.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:48.529][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.530][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.530][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:48.530][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:48.531][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.531][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:48.532][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:48.532][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.533][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[2024-07-01 12:53:48.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.534][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[2024-07-01 12:53:48.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.536][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[2024-07-01 12:53:48.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.537][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[2024-07-01 12:53:48.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.539][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[2024-07-01 12:53:48.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.540][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[2024-07-01 12:53:48.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.542][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[2024-07-01 12:53:48.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.543][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[2024-07-01 12:53:48.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.545][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[2024-07-01 12:53:48.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.546][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[2024-07-01 12:53:48.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.548][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[2024-07-01 12:53:48.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.549][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[2024-07-01 12:53:48.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.551][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[2024-07-01 12:53:48.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.552][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[2024-07-01 12:53:48.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.553][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[2024-07-01 12:53:48.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.555][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[2024-07-01 12:53:48.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.556][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[2024-07-01 12:53:48.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.558][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[2024-07-01 12:53:48.558][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-01 12:53:48.559][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-01 12:53:48.560][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-01 12:53:48.562][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-01 12:53:48.563][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-01 12:53:48.564][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-01 12:53:48.565][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-01 12:53:48.565][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-01 12:53:48.566][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-01 12:53:48.566][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-01 12:53:48.567][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-01 12:53:48.567][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-01 12:53:48.568][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-01 12:53:48.568][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-01 12:53:48.569][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-01 12:53:48.569][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-01 12:53:48.570][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-01 12:53:48.570][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-01 12:53:48.571][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-01 12:53:48.572][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-01 12:53:48.572][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-01 12:53:48.573][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-01 12:53:48.573][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-01 12:53:48.574][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-01 12:53:48.574][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-01 12:53:48.575][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-01 12:53:48.575][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-01 12:53:48.575][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-01 12:53:48.576][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-01 12:53:48.577][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-01 12:53:48.577][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-01 12:53:48.578][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-01 12:53:48.578][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-01 12:53:48.579][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-01 12:53:48.580][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-01 12:53:48.581][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-01 12:53:48.582][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-01 12:53:48.582][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-01 12:53:48.583][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-01 12:53:48.583][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-01 12:53:48.584][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-01 12:53:48.584][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-01 12:53:48.585][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-01 12:53:48.585][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-01 12:53:48.587][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-01 12:53:48.588][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-01 12:53:48.589][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-01 12:53:48.590][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-01 12:53:48.590][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-01 12:53:48.591][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-01 12:53:48.593][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-01 12:53:48.594][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-01 12:53:48.596][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-01 12:53:48.597][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-01 12:53:48.598][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-01 12:53:48.599][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-01 12:53:48.599][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-01 12:53:48.600][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-01 12:53:48.600][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-01 12:53:48.601][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-01 12:53:48.601][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-01 12:53:48.602][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-01 12:53:48.602][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-01 12:53:48.603][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-01 12:53:48.604][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-01 12:53:48.604][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-01 12:53:48.605][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-01 12:53:48.605][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-01 12:53:48.605][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-01 12:53:48.606][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-01 12:53:48.606][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-01 12:53:48.607][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-01 12:53:48.607][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-01 12:53:48.608][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-01 12:53:48.608][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-01 12:53:48.609][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-01 12:53:48.615][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-01 12:53:48.617][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-01 12:53:48.619][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-01 12:53:48.620][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-01 12:53:48.620][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-01 12:53:48.621][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-01 12:53:48.621][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-01 12:53:48.622][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-01 12:53:48.623][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-01 12:53:48.623][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:48.624][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.624][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.624][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[2024-07-01 12:53:48.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.626][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[2024-07-01 12:53:48.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.628][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[2024-07-01 12:53:48.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.630][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[2024-07-01 12:53:48.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.632][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[2024-07-01 12:53:48.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.634][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[2024-07-01 12:53:48.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.636][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[2024-07-01 12:53:48.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.638][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[2024-07-01 12:53:48.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.640][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[2024-07-01 12:53:48.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.645][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[2024-07-01 12:53:48.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.650][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[2024-07-01 12:53:48.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.655][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[2024-07-01 12:53:48.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.660][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[2024-07-01 12:53:48.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.662][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[2024-07-01 12:53:48.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.666][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[2024-07-01 12:53:48.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.672][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[2024-07-01 12:53:48.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.678][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[2024-07-01 12:53:48.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:48.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:48.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:48.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:48.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:48.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:48.682][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[2024-07-01 12:53:48.683][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-01 12:53:48.683][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-01 12:53:48.684][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.685][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.685][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.685][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:48.686][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.686][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.687][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.688][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-01 12:53:48.688][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-01 12:53:48.689][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:48.689][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.689][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-01 12:53:48.690][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:48.691][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:48.691][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:48.691][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:48.691][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-01 12:53:48.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:48.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:48.694][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:48.695][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:48.696][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:48.697][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:48.698][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:48.698][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-01 12:53:48.699][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:48.699][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:48.700][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:48.700][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-01 12:53:48.700][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-01 12:53:48.702][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-01 12:53:48.703][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-01 12:53:48.705][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-01 12:53:48.706][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-01 12:53:48.707][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-01 12:53:48.708][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-01 12:53:48.710][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-01 12:53:48.711][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-01 12:53:48.712][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-01 12:53:48.713][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-01 12:53:48.714][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-01 12:53:48.714][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-01 12:53:48.714][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-01 12:53:48.715][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-01 12:53:48.716][biodb::testThat]
biodb.INFO [2024-07-01 12:53:48.716][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-07-01 12:53:48.716][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:48.717][biodb::testThat]
biodb.DEBUG[2024-07-01 12:53:48.719][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-01 12:53:48.723][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:48.724][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:48.725][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-07-01 12:53:48.791][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-07-01 12:53:48.869][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:48.872][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-07-01 12:53:48.875][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-07-01 12:53:48.880][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:48.883][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:48.884][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:48.885][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:48.960][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:49.033][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:49.035][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-07-01 12:53:49.040][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-07-01 12:53:49.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:49.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:49.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:49.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:49.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:49.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:49.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:49.054][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:49.058][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:49.059][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:49.060][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:49.134][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:49.205][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:49.208][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-07-01 12:53:49.213][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-07-01 12:53:49.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:49.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:49.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:49.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:49.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:49.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:49.226][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[2024-07-01 12:53:49.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:49.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:49.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:49.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:49.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:49.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:49.251][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[2024-07-01 12:53:49.257][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:49.261][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:49.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-07-01 12:53:49.264][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:49.265][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-07-01 12:53:49.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:49.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:49.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:49.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:49.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:49.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:49.278][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[2024-07-01 12:53:49.280][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:49.284][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:49.285][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-07-01 12:53:49.286][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:49.287][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-07-01 12:53:49.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:49.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:49.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:49.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:49.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:49.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:49.298][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[2024-07-01 12:53:49.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:49.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:49.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:49.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:49.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:49.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:49.315][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[2024-07-01 12:53:49.327][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:49.331][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:49.332][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-07-01 12:53:49.333][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:49.335][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-07-01 12:53:49.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:49.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:49.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:49.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:49.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:49.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:49.346][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[2024-07-01 12:53:49.348][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:49.351][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:49.352][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-07-01 12:53:49.353][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:49.354][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-07-01 12:53:49.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:49.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:49.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:49.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:49.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:49.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:49.366][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[2024-07-01 12:53:49.368][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:49.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:49.372][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-01 12:53:49.373][rule$waitAsNeeded] Wait 0.351692 second(s).
biodb.TRACE[2024-07-01 12:53:49.877][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:49.950][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:50.030][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:50.033][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-07-01 12:53:50.037][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-07-01 12:53:50.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:50.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.050][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 [2024-07-01 12:53:50.057][biodb::testThat]
biodb.INFO [2024-07-01 12:53:50.058][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-07-01 12:53:50.059][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:50.060][biodb::testThat]
biodb.DEBUG[2024-07-01 12:53:50.063][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:50.067][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:50.068][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:50.070][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:50.210][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:50.284][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:50.286][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-07-01 12:53:50.291][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-07-01 12:53:50.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:50.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:50.309][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:50.313][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:50.314][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:50.316][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:50.387][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:50.457][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:50.460][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-07-01 12:53:50.464][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-07-01 12:53:50.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:50.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.476][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 [2024-07-01 12:53:50.481][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-01 12:53:50.482][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-01 12:53:50.483][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-01 12:53:50.484][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-01 12:53:50.485][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.486][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.488][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.488][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 [2024-07-01 12:53:50.492][biodb::testContext]
biodb.INFO [2024-07-01 12:53:50.493][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-01 12:53:50.494][biodb::testContext] Test context - Test web services
biodb.INFO [2024-07-01 12:53:50.495][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-01 12:53:50.496][biodb::testContext]
biodb.INFO [2024-07-01 12:53:50.498][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-01 12:53:50.500][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-01 12:53:50.505][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:50.506][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-01 12:53:50.507][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-01 12:53:50.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:50.510][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-01 12:53:50.511][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-01 12:53:50.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.514][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[2024-07-01 12:53:50.515][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-01 12:53:50.516][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-01 12:53:50.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:50.519][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-01 12:53:50.520][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-01 12:53:50.521][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-01 12:53:50.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.524][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[2024-07-01 12:53:50.524][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-01 12:53:50.525][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-01 12:53:50.526][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-01 12:53:50.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:50.529][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-01 12:53:50.530][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-01 12:53:50.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.532][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[2024-07-01 12:53:50.533][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-01 12:53:50.534][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-01 12:53:50.535][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-01 12:53:50.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:50.538][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-01 12:53:50.539][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-01 12:53:50.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.541][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[2024-07-01 12:53:50.542][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-01 12:53:50.543][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-01 12:53:50.544][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-01 12:53:50.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:50.547][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-01 12:53:50.548][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-01 12:53:50.549][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-01 12:53:50.549][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-01 12:53:50.550][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-01 12:53:50.551][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-01 12:53:50.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.553][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[2024-07-01 12:53:50.554][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-01 12:53:50.555][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-01 12:53:50.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:50.558][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-01 12:53:50.559][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-01 12:53:50.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.561][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[2024-07-01 12:53:50.562][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-01 12:53:50.563][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-01 12:53:50.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:50.566][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-01 12:53:50.567][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-01 12:53:50.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.569][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[2024-07-01 12:53:50.570][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-01 12:53:50.571][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-01 12:53:50.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:50.574][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-01 12:53:50.575][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-01 12:53:50.589][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-01 12:53:50.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.592][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[2024-07-01 12:53:50.592][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-01 12:53:50.593][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-01 12:53:50.594][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-01 12:53:50.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:50.597][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-01 12:53:50.599][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.600][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-01 12:53:50.601][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.602][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:50.602][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.603][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.604][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.605][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.606][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-01 12:53:50.606][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:50.607][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.608][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-01 12:53:50.609][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:50.610][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.611][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.611][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:50.611][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:50.611][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:50.611][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-01 12:53:50.611][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-01 12:53:50.612][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:50.613][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:50.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:50.615][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:50.615][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:50.616][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:50.617][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.618][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.619][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:50.619][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:50.620][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.621][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.622][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-01 12:53:50.624][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.625][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-01 12:53:50.626][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.626][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:50.627][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.628][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.629][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.630][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.630][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-01 12:53:50.631][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:50.632][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.633][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-01 12:53:50.634][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:50.635][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.635][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.636][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:50.636][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:50.636][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:50.636][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-01 12:53:50.636][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-01 12:53:50.637][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:50.638][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:50.639][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:50.639][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:50.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:50.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:50.642][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.643][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.643][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:50.644][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:50.645][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.646][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.647][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-01 12:53:50.648][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.649][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-01 12:53:50.650][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.651][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:50.652][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.653][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.654][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.654][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.655][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-01 12:53:50.656][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:50.657][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.658][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-01 12:53:50.659][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:50.659][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.660][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.661][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.662][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:50.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:50.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:50.680][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:50.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:50.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:50.683][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.684][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.684][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:50.685][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:50.686][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.687][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.688][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-01 12:53:50.689][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.690][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-01 12:53:50.691][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.692][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:50.693][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.694][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.694][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.696][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-01 12:53:50.697][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:50.698][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.698][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-01 12:53:50.699][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:50.700][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.701][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:50.701][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.702][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:50.703][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:50.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:50.705][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:50.705][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:50.706][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:50.707][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:50.708][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.708][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:50.709][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:50.710][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:50.711][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:50.712][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:50.713][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.713][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[2024-07-01 12:53:50.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.718][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[2024-07-01 12:53:50.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.722][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[2024-07-01 12:53:50.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.727][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[2024-07-01 12:53:50.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.731][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[2024-07-01 12:53:50.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.736][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[2024-07-01 12:53:50.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.741][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[2024-07-01 12:53:50.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.746][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[2024-07-01 12:53:50.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.751][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[2024-07-01 12:53:50.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.756][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[2024-07-01 12:53:50.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.760][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[2024-07-01 12:53:50.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.765][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[2024-07-01 12:53:50.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.770][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[2024-07-01 12:53:50.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.776][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[2024-07-01 12:53:50.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.782][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[2024-07-01 12:53:50.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.786][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[2024-07-01 12:53:50.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.791][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[2024-07-01 12:53:50.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.794][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[2024-07-01 12:53:50.795][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-01 12:53:50.797][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-01 12:53:50.798][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-01 12:53:50.799][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-01 12:53:50.801][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-01 12:53:50.802][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-01 12:53:50.803][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-01 12:53:50.804][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-01 12:53:50.806][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-01 12:53:50.807][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-01 12:53:50.808][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-01 12:53:50.809][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-01 12:53:50.810][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-01 12:53:50.812][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-01 12:53:50.813][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-01 12:53:50.815][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-01 12:53:50.816][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-01 12:53:50.818][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-01 12:53:50.819][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-01 12:53:50.820][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-01 12:53:50.821][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-01 12:53:50.823][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-01 12:53:50.824][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-01 12:53:50.825][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-01 12:53:50.826][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-01 12:53:50.827][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-01 12:53:50.828][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-01 12:53:50.829][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-01 12:53:50.831][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-01 12:53:50.832][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-01 12:53:50.833][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-01 12:53:50.834][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-01 12:53:50.835][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-01 12:53:50.836][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-01 12:53:50.837][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-01 12:53:50.839][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-01 12:53:50.840][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-01 12:53:50.841][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-01 12:53:50.842][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-01 12:53:50.843][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-01 12:53:50.844][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-01 12:53:50.846][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-01 12:53:50.847][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-01 12:53:50.848][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-01 12:53:50.849][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-01 12:53:50.850][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-01 12:53:50.851][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-01 12:53:50.852][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-01 12:53:50.854][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-01 12:53:50.856][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-01 12:53:50.857][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-01 12:53:50.859][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-01 12:53:50.860][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-01 12:53:50.861][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-01 12:53:50.863][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-01 12:53:50.864][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-01 12:53:50.865][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-01 12:53:50.866][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-01 12:53:50.868][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-01 12:53:50.869][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-01 12:53:50.870][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-01 12:53:50.871][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-01 12:53:50.873][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-01 12:53:50.874][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-01 12:53:50.875][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-01 12:53:50.876][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-01 12:53:50.878][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-01 12:53:50.879][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-01 12:53:50.880][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-01 12:53:50.882][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-01 12:53:50.883][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-01 12:53:50.885][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-01 12:53:50.886][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-01 12:53:50.887][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-01 12:53:50.888][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-01 12:53:50.889][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-01 12:53:50.891][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-01 12:53:50.892][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-01 12:53:50.893][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-01 12:53:50.894][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-01 12:53:50.895][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-01 12:53:50.897][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-01 12:53:50.898][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-01 12:53:50.899][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-01 12:53:50.901][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-01 12:53:50.902][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:50.903][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.905][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.906][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[2024-07-01 12:53:50.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.911][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[2024-07-01 12:53:50.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.916][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[2024-07-01 12:53:50.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.921][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[2024-07-01 12:53:50.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.927][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[2024-07-01 12:53:50.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.932][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[2024-07-01 12:53:50.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.937][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[2024-07-01 12:53:50.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.942][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[2024-07-01 12:53:50.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.947][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[2024-07-01 12:53:50.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.952][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[2024-07-01 12:53:50.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.958][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[2024-07-01 12:53:50.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.963][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[2024-07-01 12:53:50.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.968][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[2024-07-01 12:53:50.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.981][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[2024-07-01 12:53:50.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.986][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[2024-07-01 12:53:50.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.991][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[2024-07-01 12:53:50.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:50.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:50.996][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[2024-07-01 12:53:50.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:50.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:50.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:50.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:50.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.001][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[2024-07-01 12:53:51.003][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-01 12:53:51.005][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-01 12:53:51.007][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.008][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.009][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.010][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:51.011][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.011][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.012][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.013][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-01 12:53:51.014][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-01 12:53:51.015][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:51.016][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.017][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-01 12:53:51.018][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:51.019][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-01 12:53:51.019][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-01 12:53:51.019][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-01 12:53:51.019][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-01 12:53:51.019][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-01 12:53:51.019][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-01 12:53:51.019][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-01 12:53:51.019][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-01 12:53:51.019][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-01 12:53:51.019][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-01 12:53:51.019][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-01 12:53:51.020][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.021][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:51.021][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:51.021][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:51.022][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-01 12:53:51.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.024][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.024][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:51.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.027][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.028][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:51.028][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-01 12:53:51.028][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:51.029][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:51.030][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.031][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-01 12:53:51.031][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-01 12:53:51.032][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-01 12:53:51.033][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-01 12:53:51.035][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-01 12:53:51.036][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-01 12:53:51.038][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-01 12:53:51.039][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-01 12:53:51.042][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-01 12:53:51.043][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-01 12:53:51.044][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-01 12:53:51.046][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-01 12:53:51.047][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-01 12:53:51.048][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-01 12:53:51.049][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-01 12:53:51.050][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-01 12:53:51.051][biodb::testThat]
biodb.INFO [2024-07-01 12:53:51.052][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-07-01 12:53:51.053][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:51.054][biodb::testThat]
biodb.DEBUG[2024-07-01 12:53:51.057][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-01 12:53:51.061][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:51.062][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-01 12:53:51.063][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:51.065][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-01 12:53:51.068][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:51.071][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:51.072][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:51.074][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-01 12:53:51.153][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-01 12:53:51.227][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:51.230][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-07-01 12:53:51.234][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-07-01 12:53:51.243][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-01 12:53:51.245][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-01 12:53:51.246][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-01 12:53:51.247][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-01 12:53:51.247][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.249][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.251][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-01 12:53:51.255][biodb::testContext]
biodb.INFO [2024-07-01 12:53:51.256][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-01 12:53:51.257][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-07-01 12:53:51.258][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-01 12:53:51.259][biodb::testContext]
biodb.INFO [2024-07-01 12:53:51.261][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-01 12:53:51.263][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-01 12:53:51.268][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:51.269][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-01 12:53:51.270][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-01 12:53:51.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.273][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[2024-07-01 12:53:51.274][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-01 12:53:51.275][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-01 12:53:51.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:51.278][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-01 12:53:51.279][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-01 12:53:51.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.281][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[2024-07-01 12:53:51.282][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-01 12:53:51.282][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-01 12:53:51.283][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-01 12:53:51.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:51.286][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-01 12:53:51.287][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-01 12:53:51.288][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-01 12:53:51.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.290][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[2024-07-01 12:53:51.291][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-01 12:53:51.292][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-01 12:53:51.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:51.295][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-01 12:53:51.296][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-01 12:53:51.297][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-01 12:53:51.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.299][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[2024-07-01 12:53:51.299][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-01 12:53:51.300][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-01 12:53:51.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:51.303][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-01 12:53:51.304][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-01 12:53:51.305][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-01 12:53:51.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.307][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[2024-07-01 12:53:51.308][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-01 12:53:51.308][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-01 12:53:51.309][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-01 12:53:51.310][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-01 12:53:51.311][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-01 12:53:51.312][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-01 12:53:51.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:51.314][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-01 12:53:51.315][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-01 12:53:51.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.317][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[2024-07-01 12:53:51.318][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-01 12:53:51.319][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-01 12:53:51.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:51.322][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-01 12:53:51.323][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-01 12:53:51.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.325][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[2024-07-01 12:53:51.325][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-01 12:53:51.326][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-01 12:53:51.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:51.329][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-01 12:53:51.330][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-01 12:53:51.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.332][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[2024-07-01 12:53:51.333][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-01 12:53:51.334][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-01 12:53:51.349][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-01 12:53:51.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:51.353][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-01 12:53:51.354][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-01 12:53:51.355][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-01 12:53:51.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.357][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[2024-07-01 12:53:51.358][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-01 12:53:51.360][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.360][self$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[2024-07-01 12:53:51.361][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.362][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:51.363][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.364][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.365][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.365][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.366][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-01 12:53:51.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:51.368][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.369][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-01 12:53:51.369][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:51.370][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.371][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.372][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:51.372][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:51.372][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:51.372][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-01 12:53:51.372][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-01 12:53:51.373][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:51.374][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.375][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:51.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.377][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.378][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.379][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:51.380][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:51.380][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.381][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.382][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-01 12:53:51.384][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.385][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-01 12:53:51.385][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.386][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:51.387][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.388][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.389][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.390][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.390][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-01 12:53:51.391][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:51.392][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.393][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-01 12:53:51.393][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:51.394][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.395][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.396][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:51.396][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:51.396][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:51.396][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-01 12:53:51.396][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-01 12:53:51.397][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:51.398][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.398][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.399][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:51.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.400][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.401][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.402][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.403][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:51.403][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:51.404][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.405][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.406][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-01 12:53:51.408][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.408][self$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[2024-07-01 12:53:51.409][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.410][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:51.411][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.412][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.412][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.413][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.414][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-01 12:53:51.415][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:51.416][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.416][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-01 12:53:51.417][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:51.418][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.419][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.420][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.420][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:51.421][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.422][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.423][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:51.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.424][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.425][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.426][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.426][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:51.427][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:51.428][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.429][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.430][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-01 12:53:51.431][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.432][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-01 12:53:51.433][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.434][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:51.435][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.435][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.449][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.450][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.451][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-01 12:53:51.452][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:51.453][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.454][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-01 12:53:51.455][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:51.455][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.456][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.457][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.458][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-01 12:53:51.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.460][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:51.461][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.462][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.462][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.463][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.464][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:51.465][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:51.466][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.466][self$setPropertyValue]
biodb.DEBUG[2024-07-01 12:53:51.468][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:51.468][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.469][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[2024-07-01 12:53:51.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.473][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[2024-07-01 12:53:51.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.476][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[2024-07-01 12:53:51.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.480][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[2024-07-01 12:53:51.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.483][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[2024-07-01 12:53:51.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.487][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[2024-07-01 12:53:51.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.490][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[2024-07-01 12:53:51.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.494][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[2024-07-01 12:53:51.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.498][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[2024-07-01 12:53:51.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.501][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[2024-07-01 12:53:51.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.504][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[2024-07-01 12:53:51.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.508][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[2024-07-01 12:53:51.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.512][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[2024-07-01 12:53:51.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.517][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[2024-07-01 12:53:51.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.520][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[2024-07-01 12:53:51.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.524][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[2024-07-01 12:53:51.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.528][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[2024-07-01 12:53:51.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.531][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[2024-07-01 12:53:51.532][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-01 12:53:51.534][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-01 12:53:51.535][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-01 12:53:51.536][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-01 12:53:51.537][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-01 12:53:51.539][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-01 12:53:51.540][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-01 12:53:51.541][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-01 12:53:51.542][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-01 12:53:51.543][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-01 12:53:51.545][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-01 12:53:51.546][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-01 12:53:51.547][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-01 12:53:51.548][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-01 12:53:51.549][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-01 12:53:51.551][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-01 12:53:51.552][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-01 12:53:51.553][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-01 12:53:51.554][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-01 12:53:51.555][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-01 12:53:51.557][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-01 12:53:51.558][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-01 12:53:51.559][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-01 12:53:51.560][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-01 12:53:51.561][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-01 12:53:51.562][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-01 12:53:51.564][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-01 12:53:51.565][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-01 12:53:51.566][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-01 12:53:51.567][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-01 12:53:51.568][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-01 12:53:51.569][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-01 12:53:51.571][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-01 12:53:51.572][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-01 12:53:51.573][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-01 12:53:51.574][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-01 12:53:51.575][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-01 12:53:51.576][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-01 12:53:51.578][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-01 12:53:51.579][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-01 12:53:51.580][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-01 12:53:51.582][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-01 12:53:51.583][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-01 12:53:51.585][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-01 12:53:51.586][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-01 12:53:51.587][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-01 12:53:51.589][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-01 12:53:51.591][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-01 12:53:51.593][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-01 12:53:51.594][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-01 12:53:51.595][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-01 12:53:51.596][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-01 12:53:51.597][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-01 12:53:51.598][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-01 12:53:51.600][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-01 12:53:51.601][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-01 12:53:51.602][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-01 12:53:51.603][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-01 12:53:51.604][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-01 12:53:51.606][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-01 12:53:51.607][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-01 12:53:51.608][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-01 12:53:51.609][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-01 12:53:51.611][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-01 12:53:51.612][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-01 12:53:51.613][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-01 12:53:51.615][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-01 12:53:51.616][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-01 12:53:51.617][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-01 12:53:51.618][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-01 12:53:51.620][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-01 12:53:51.621][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-01 12:53:51.622][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-01 12:53:51.624][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-01 12:53:51.625][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-01 12:53:51.626][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-01 12:53:51.627][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-01 12:53:51.628][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-01 12:53:51.630][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-01 12:53:51.631][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-01 12:53:51.632][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-01 12:53:51.634][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-01 12:53:51.635][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-01 12:53:51.637][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-01 12:53:51.639][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-01 12:53:51.640][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-01 12:53:51.641][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.642][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.643][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[2024-07-01 12:53:51.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.648][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[2024-07-01 12:53:51.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.653][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[2024-07-01 12:53:51.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.658][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[2024-07-01 12:53:51.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.664][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[2024-07-01 12:53:51.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.669][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[2024-07-01 12:53:51.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.674][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[2024-07-01 12:53:51.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.679][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[2024-07-01 12:53:51.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.685][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[2024-07-01 12:53:51.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.690][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[2024-07-01 12:53:51.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.695][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[2024-07-01 12:53:51.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.700][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[2024-07-01 12:53:51.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.705][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[2024-07-01 12:53:51.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.710][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[2024-07-01 12:53:51.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.715][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[2024-07-01 12:53:51.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.720][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[2024-07-01 12:53:51.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.734][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[2024-07-01 12:53:51.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-01 12:53:51.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.739][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[2024-07-01 12:53:51.741][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-01 12:53:51.743][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-01 12:53:51.745][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.746][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.747][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.748][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-01 12:53:51.749][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.749][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.750][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.751][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-01 12:53:51.752][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-01 12:53:51.753][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-01 12:53:51.753][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.754][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-01 12:53:51.755][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-01 12:53:51.756][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-01 12:53:51.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-01 12:53:51.756][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-01 12:53:51.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-01 12:53:51.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-01 12:53:51.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-01 12:53:51.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-01 12:53:51.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-01 12:53:51.756][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-01 12:53:51.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-01 12:53:51.756][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-01 12:53:51.757][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-01 12:53:51.758][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-01 12:53:51.758][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-01 12:53:51.758][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-01 12:53:51.759][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-01 12:53:51.760][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.761][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.762][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-01 12:53:51.763][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-01 12:53:51.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-01 12:53:51.764][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-01 12:53:51.765][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:51.765][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-01 12:53:51.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-01 12:53:51.766][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-01 12:53:51.767][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-01 12:53:51.768][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-01 12:53:51.768][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-01 12:53:51.769][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-01 12:53:51.771][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-01 12:53:51.773][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-01 12:53:51.775][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-01 12:53:51.776][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-01 12:53:51.777][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-01 12:53:51.781][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-01 12:53:51.782][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-01 12:53:51.783][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-01 12:53:51.784][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-01 12:53:51.785][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-01 12:53:51.786][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-01 12:53:51.787][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-01 12:53:51.788][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-01 12:53:51.789][biodb::testThat]
biodb.INFO [2024-07-01 12:53:51.790][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-07-01 12:53:51.791][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-01 12:53:51.792][biodb::testThat]
biodb.DEBUG[2024-07-01 12:53:51.795][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-01 12:53:51.798][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:51.799][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-01 12:53:51.801][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:51.802][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-01 12:53:51.805][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-01 12:53:51.809][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-01 12:53:51.810][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-07-01 12:53:51.811][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-01 12:53:51.813][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-07-01 12:53:51.817][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-07-01 12:53:51.818][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-01 12:53:51.820][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-07-01 12:53:51.821][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-01 12:53:51.822][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-01 12:53:51.823][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-01 12:53:51.823][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-01 12:53:51.824][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-01 12:53:51.825][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-01 12:53:51.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:51.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:51.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:51.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:51.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:51.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:51.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-01 12:53:51.838][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-07-01 12:53:51.841][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-01 12:53:51.842][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-01 12:53:51.843][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-07-01 12:53:52.302][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-07-01 12:53:52.478][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-01 12:53:52.480][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-07-01 12:53:52.482][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-07-01 12:53:52.484][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-07-01 12:53:52.485][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-01 12:53:52.485][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-01 12:53:52.486][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-01 12:53:52.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-01 12:53:52.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:52.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:52.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:52.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:52.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:52.491][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[2024-07-01 12:53:52.494][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:52.494][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:52.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.495][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:52.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:52.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.497][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:52.498][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:52.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.498][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.499][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-01 12:53:52.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-01 12:53:52.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.500][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:52.501][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:52.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.501][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.502][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-01 12:53:52.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-01 12:53:52.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.503][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-01 12:53:52.504][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-01 12:53:52.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.504][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.505][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-01 12:53:52.506][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-01 12:53:52.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.507][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.507][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:52.508][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:52.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.509][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.509][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:52.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-01 12:53:52.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.511][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:52.513][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:52.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.514][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.516][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-01 12:53:52.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-01 12:53:52.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.519][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:52.520][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:52.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.522][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:52.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-01 12:53:52.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.525][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:52.525][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:52.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.526][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-01 12:53:52.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-01 12:53:52.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.528][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:52.528][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:52.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.529][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.530][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-01 12:53:52.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-01 12:53:52.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.532][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:52.532][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:52.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.533][ef$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.534][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-01 12:53:52.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-01 12:53:52.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:52.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:52.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:52.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:52.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:52.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:52.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-01 12:53:52.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-01 12:53:52.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:52.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:52.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:52.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:52.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:52.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:52.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:52.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:52.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:52.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:52.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-01 12:53:52.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-01 12:53:52.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-01 12:53:52.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-01 12:53:52.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-01 12:53:52.551][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-07-01 12:53:52.553][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-01 12:53:52.554][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-01 12:53:52.555][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-01 12:53:52.555][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-01 12:53:52.555][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-01 12:53:52.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-01 12:53:52.556][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-01 12:53:52.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-01 12:53:52.556][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-01 12:53:52.557][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 386 ]
>
> proc.time()
user system elapsed
17.073 1.050 28.338
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.446 | 0.651 | 3.245 | |
| ChebiEntry | 0.426 | 0.017 | 0.448 | |