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This page was generated on 2025-04-22 13:17 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 206/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_21
git_last_commit: b8d718f
git_last_commit_date: 2025-04-15 12:39:10 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for biodbChebi on kjohnson3

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.

raw results


Summary

Package: biodbChebi
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2025-04-21 18:22:36 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 18:23:37 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 61.8 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.14.0’
* 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

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.14.0’
** 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)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 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 [2025-04-21 18:22:57.884][biodb::testContext]
biodb.INFO [2025-04-21 18:22:57.886][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 18:22:57.886][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-04-21 18:22:57.886][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 18:22:57.887][biodb::testContext]
biodb.INFO [2025-04-21 18:22:57.889][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-21 18:22:57.890][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-21 18:22:57.893][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:22:57.894][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-21 18:22:57.894][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-21 18:22:57.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.895][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-21 18:22:57.901][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-21 18:22:57.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.902][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[2025-04-21 18:22:57.902][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-21 18:22:57.902][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-21 18:22:57.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.903][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-21 18:22:57.903][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-21 18:22:57.904][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-21 18:22:57.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.904][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.DEBUG[2025-04-21 18:22:57.905][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-21 18:22:57.905][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-21 18:22:57.905][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-21 18:22:57.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.906][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-21 18:22:57.906][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-21 18:22:57.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.907][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-21 18:22:57.908][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-21 18:22:57.908][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-21 18:22:57.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.909][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-21 18:22:57.909][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-21 18:22:57.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.910][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-21 18:22:57.910][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-21 18:22:57.910][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-21 18:22:57.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.911][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-21 18:22:57.912][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-21 18:22:57.912][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-21 18:22:57.912][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-21 18:22:57.912][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-21 18:22:57.913][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-21 18:22:57.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.913][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[2025-04-21 18:22:57.914][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-21 18:22:57.914][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-21 18:22:57.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.915][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-21 18:22:57.915][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-21 18:22:57.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.916][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[2025-04-21 18:22:57.916][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-21 18:22:57.916][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-21 18:22:57.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.917][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-21 18:22:57.917][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-21 18:22:57.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.918][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-21 18:22:57.919][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-21 18:22:57.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.920][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-21 18:22:57.920][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-21 18:22:57.927][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-21 18:22:57.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.928][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-21 18:22:57.928][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-21 18:22:57.929][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-21 18:22:57.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.931][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-21 18:22:57.942][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.951][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-21 18:22:57.951][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.951][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:22:57.952][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.952][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.952][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.953][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.953][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 18:22:57.953][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:22:57.953][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.954][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-21 18:22:57.954][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:22:57.954][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.954][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.955][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:22:57.955][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:22:57.955][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:22:57.955][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 18:22:57.955][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 18:22:57.955][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:22:57.955][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:22:57.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:22:57.956][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:22:57.956][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:22:57.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:22:57.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.957][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.957][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:22:57.957][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:22:57.957][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.958][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.958][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-21 18:22:57.959][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.959][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 18:22:57.959][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:22:57.960][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.960][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.960][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.960][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.961][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 18:22:57.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:22:57.961][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.962][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-21 18:22:57.962][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:22:57.962][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.962][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.963][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:22:57.963][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:22:57.963][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:22:57.963][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 18:22:57.963][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 18:22:57.963][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:22:57.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:22:57.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:22:57.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:22:57.964][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:22:57.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:22:57.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.965][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.965][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:22:57.965][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:22:57.965][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.965][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.966][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-21 18:22:57.966][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.967][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-21 18:22:57.967][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.967][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:22:57.967][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.968][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.968][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.968][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.968][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 18:22:57.969][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:22:57.969][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.969][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-21 18:22:57.969][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:22:57.970][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.970][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.970][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.970][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:22:57.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:22:57.971][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:22:57.971][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:22:57.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:22:57.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:22:57.972][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.972][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.972][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:22:57.973][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:22:57.973][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.973][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.973][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-21 18:22:57.974][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.974][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 18:22:57.974][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.975][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:22:57.975][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.975][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.975][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.976][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.976][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 18:22:57.976][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:22:57.976][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.977][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-21 18:22:57.977][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:22:57.977][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.977][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:57.978][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.978][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:22:57.978][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:22:57.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:22:57.979][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:22:57.979][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:22:57.979][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:22:57.979][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:22:57.980][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.980][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:22:57.980][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:22:57.980][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:57.981][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:22:57.982][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:22:57.982][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.986][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[2025-04-21 18:22:57.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.991][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[2025-04-21 18:22:57.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:57.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.998][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.DEBUG[2025-04-21 18:22:57.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:57.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:57.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:57.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:57.999][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[2025-04-21 18:22:57.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.001][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[2025-04-21 18:22:58.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.003][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.DEBUG[2025-04-21 18:22:58.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.005][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-21 18:22:58.007][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-21 18:22:58.008][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-21 18:22:58.008][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-21 18:22:58.008][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 18:22:58.009][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-21 18:22:58.009][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-21 18:22:58.009][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-21 18:22:58.010][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-21 18:22:58.010][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-21 18:22:58.011][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 18:22:58.011][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-21 18:22:58.011][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-21 18:22:58.012][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-21 18:22:58.012][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-21 18:22:58.012][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-21 18:22:58.013][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-21 18:22:58.013][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-21 18:22:58.014][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 18:22:58.014][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-21 18:22:58.014][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-21 18:22:58.015][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-21 18:22:58.015][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-21 18:22:58.015][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-21 18:22:58.016][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-21 18:22:58.016][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-21 18:22:58.017][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-21 18:22:58.017][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-21 18:22:58.017][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-21 18:22:58.018][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-21 18:22:58.018][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-21 18:22:58.018][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-21 18:22:58.019][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-21 18:22:58.019][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-21 18:22:58.019][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-21 18:22:58.020][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-21 18:22:58.020][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-21 18:22:58.021][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-21 18:22:58.021][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-21 18:22:58.021][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-21 18:22:58.022][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-21 18:22:58.022][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-21 18:22:58.022][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-21 18:22:58.023][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-21 18:22:58.023][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-21 18:22:58.024][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-21 18:22:58.024][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-21 18:22:58.024][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-21 18:22:58.025][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-21 18:22:58.025][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-21 18:22:58.025][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-21 18:22:58.026][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-21 18:22:58.026][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-21 18:22:58.026][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-21 18:22:58.027][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-21 18:22:58.027][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-21 18:22:58.028][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-21 18:22:58.028][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-21 18:22:58.028][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-21 18:22:58.029][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-21 18:22:58.029][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-21 18:22:58.029][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-21 18:22:58.030][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-21 18:22:58.030][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-21 18:22:58.031][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-21 18:22:58.031][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-21 18:22:58.031][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 18:22:58.032][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 18:22:58.032][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-21 18:22:58.032][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-21 18:22:58.033][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-21 18:22:58.033][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-21 18:22:58.033][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-21 18:22:58.034][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-21 18:22:58.034][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-21 18:22:58.035][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-21 18:22:58.035][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-21 18:22:58.035][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-21 18:22:58.036][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-21 18:22:58.036][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-21 18:22:58.036][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-21 18:22:58.037][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-21 18:22:58.038][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-21 18:22:58.040][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-21 18:22:58.041][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-21 18:22:58.042][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:22:58.042][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.043][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.052][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[2025-04-21 18:22:58.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.054][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[2025-04-21 18:22:58.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.061][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[2025-04-21 18:22:58.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.064][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[2025-04-21 18:22:58.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.069][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[2025-04-21 18:22:58.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:22:58.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:22:58.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.075][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.DEBUG[2025-04-21 18:22:58.075][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-21 18:22:58.079][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-21 18:22:58.079][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:58.080][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-21 18:22:58.080][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:58.080][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:22:58.081][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:58.081][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:22:58.081][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:58.081][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-21 18:22:58.082][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-21 18:22:58.082][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:22:58.082][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-21 18:22:58.083][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-21 18:22:58.084][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:22:58.084][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:22:58.084][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:22:58.084][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-21 18:22:58.084][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:22:58.085][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:22:58.085][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:22:58.085][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:22:58.085][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:22:58.086][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:22:58.086][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:22:58.086][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-21 18:22:58.086][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:22:58.086][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:22:58.087][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-21 18:22:58.087][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-21 18:22:58.087][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-21 18:22:58.089][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 18:22:58.089][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 18:22:58.090][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-21 18:22:58.090][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 18:22:58.091][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 18:22:58.091][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 18:22:58.101][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-21 18:22:58.102][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-21 18:22:58.103][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-21 18:22:58.105][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-21 18:22:58.124][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 18:22:58.124][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 18:22:58.125][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-21 18:22:58.125][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-21 18:22:58.129][biodb::testThat]
biodb.INFO [2025-04-21 18:22:58.130][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-21 18:22:58.130][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:22:58.130][biodb::testThat]
biodb.TRACE[2025-04-21 18:22:58.132][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-04-21 18:22:58.133][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:22:58.134][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:22:58.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:22:58.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.145][FUN] Functions in observer BiodbConfig: [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[2025-04-21 18:22:58.149][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.150][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.150][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.156][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:22:58.156][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:22:58.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.157][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.166][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:22:58.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:22:58.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.167][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:22:58.167][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:22:58.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.168][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.168][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:22:58.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:22:58.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.169][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.170][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.170][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.172][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.172][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.172][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.173][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.174][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.174][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.175][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.175][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.176][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:22:58.176][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.177][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.177][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:22:58.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.178][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.179][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.179][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.181][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.181][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.181][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.186][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.187][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:22:58.188][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.188][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.189][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:22:58.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.190][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:22:58.190][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:22:58.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.190][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.191][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:22:58.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:22:58.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:22:58.213][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-04-21 18:22:58.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.231][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.232][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.233][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-21 18:22:58.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-21 18:22:58.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.234][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-21 18:22:58.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-21 18:22:58.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.267][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.268][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.268][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.279][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.279][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.280][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.284][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.287][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.288][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.288][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.288][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.292][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:22:58.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:22:58.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.293][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:22:58.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:22:58.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:22:58.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:22:58.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.296][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:22:58.296][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:22:58.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.296][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.297][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:22:58.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:22:58.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.304][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.304][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.304][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.312][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.312][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.312][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.316][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:22:58.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:22:58.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.317][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:22:58.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:22:58.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.319][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:22:58.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:22:58.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.320][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:22:58.320][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:22:58.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.320][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.324][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:22:58.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:22:58.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.328][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.329][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.330][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.331][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.331][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.332][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.332][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.336][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.337][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.338][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.339][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.339][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.340][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.340][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.343][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:22:58.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:22:58.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.344][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:22:58.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:22:58.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.345][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:22:58.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:22:58.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.346][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:22:58.347][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:22:58.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.347][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.347][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:22:58.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:22:58.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.351][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.353][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.354][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.354][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.355][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.362][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.362][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.363][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.369][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.369][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.370][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.372][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:22:58.372][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:22:58.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.372][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.374][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:22:58.374][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:22:58.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.375][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.376][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.377][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.377][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.379][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.379][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.379][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.381][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.381][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.382][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.383][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.384][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.384][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.386][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.386][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.387][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.388][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.388][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.389][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.391][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.391][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.391][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.393][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:22:58.393][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:22:58.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.394][ef$get] fields variable is a list.
biodb.INFO [2025-04-21 18:22:58.397][biodb::testThat]
biodb.INFO [2025-04-21 18:22:58.397][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-21 18:22:58.397][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:22:58.398][biodb::testThat]
biodb.DEBUG[2025-04-21 18:22:58.402][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-04-21 18:22:58.405][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:22:58.407][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-04-21 18:22:58.407][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:22:58.408][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-04-21 18:22:58.408][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:22:58.419][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:22:58.419][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:22:58.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:22:58.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:22:58.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:22:58.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:22:58.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:22:58.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:22:58.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:22:58.424][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.425][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.425][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.432][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:22:58.433][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:22:58.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.433][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.434][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:22:58.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:22:58.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.435][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:22:58.435][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:22:58.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.436][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.436][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:22:58.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:22:58.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.437][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.437][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.438][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.439][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.439][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.440][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.440][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.441][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.442][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.442][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.442][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:22:58.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.443][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:22:58.444][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.444][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.445][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:22:58.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.446][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.446][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.446][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.448][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.448][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.449][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.450][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:22:58.450][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.451][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.451][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:22:58.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:22:58.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.452][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:22:58.452][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:22:58.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.453][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.453][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:22:58.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:22:58.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:22:58.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:22:58.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:22:58.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:22:58.468][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-04-21 18:22:58.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-21 18:22:58.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-21 18:22:58.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-21 18:22:58.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-21 18:22:58.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-21 18:22:58.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-21 18:22:58.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 18:22:58.474][biodb::testThat]
biodb.INFO [2025-04-21 18:22:58.475][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-21 18:22:58.475][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:22:58.475][biodb::testThat]
biodb.TRACE[2025-04-21 18:22:58.476][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.477][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.477][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:22:58.478][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-04-21 18:22:58.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:22:58.494][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-04-21 18:22:58.496][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-21 18:22:58.503][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:22:58.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-21 18:22:58.511][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:22:58.512][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-21 18:22:58.520][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[2025-04-21 18:22:58.522][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:22:58.522][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 18:22:58.522][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:22:58.523][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-21 18:22:58.524][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-04-21 18:22:58.529][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.529][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:22:58.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.530][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.530][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.530][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.531][ef$get] fields variable is a list.
biodb.INFO [2025-04-21 18:22:58.532][biodb::testThat]
biodb.INFO [2025-04-21 18:22:58.532][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-21 18:22:58.533][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:22:58.533][biodb::testThat]
biodb.TRACE[2025-04-21 18:22:58.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:22:58.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:22:58.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:22:58.566][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[2025-04-21 18:22:58.567][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:22:58.568][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 18:22:58.568][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:22:58.569][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-04-21 18:22:58.575][biodb::testThat]
biodb.INFO [2025-04-21 18:22:58.575][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-21 18:22:58.576][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:22:58.576][biodb::testThat]
biodb.TRACE[2025-04-21 18:22:58.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.590][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.591][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.592][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-21 18:22:58.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-21 18:22:58.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.594][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-21 18:22:58.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-21 18:22:58.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:22:58.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:22:58.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.608][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:22:58.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:22:58.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.612][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.613][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 18:22:58.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.614][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-21 18:22:58.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-21 18:22:58.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:22:58.616][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-21 18:22:58.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-21 18:22:58.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:22:58.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 18:22:58.619][biodb::testThat]
biodb.INFO [2025-04-21 18:22:58.620][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-21 18:22:58.620][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:22:58.620][biodb::testThat]
biodb.INFO [2025-04-21 18:22:58.623][biodb::testThat]
biodb.INFO [2025-04-21 18:22:58.624][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-21 18:22:58.624][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:22:58.624][biodb::testThat]
biodb.INFO [2025-04-21 18:22:58.627][biodb::testThat]
biodb.INFO [2025-04-21 18:22:58.627][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-21 18:22:58.628][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:22:58.628][biodb::testThat]
biodb.DEBUG[2025-04-21 18:22:58.629][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-04-21 18:22:59.354][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-04-21 18:23:00.596][biodb::testThat]
biodb.INFO [2025-04-21 18:23:00.597][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-21 18:23:00.597][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:00.597][biodb::testThat]
biodb.DEBUG[2025-04-21 18:23:00.943][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[2025-04-21 18:23:01.290][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:01.291][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:01.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:01.292][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:01.292][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:01.292][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:01.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:01.293][ef$get] fields variable is a list.
biodb.INFO [2025-04-21 18:23:01.294][biodb::testThat]
biodb.INFO [2025-04-21 18:23:01.294][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-04-21 18:23:01.294][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:01.295][biodb::testThat]
biodb.TRACE[2025-04-21 18:23:01.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:01.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:01.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:01.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:01.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:01.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:01.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:01.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:01.307][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:01.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:01.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:01.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:01.334][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[2025-04-21 18:23:01.336][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:01.336][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 18:23:01.337][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:01.337][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-21 18:23:01.362][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[2025-04-21 18:23:01.363][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:01.363][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 18:23:01.364][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:01.364][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-04-21 18:23:01.369][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-21 18:23:01.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-21 18:23:01.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:01.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:01.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:01.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:01.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:01.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:01.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:01.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:01.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:01.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:01.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:01.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:01.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:01.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:01.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:01.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:01.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:01.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:01.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:01.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:01.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:01.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:01.383][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[2025-04-21 18:23:01.384][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:01.385][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-21 18:23:01.385][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:01.386][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-21 18:23:01.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:01.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:01.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:01.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:01.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:01.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:01.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:01.390][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-04-21 18:23:01.405][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:01.406][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-04-21 18:23:01.406][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:01.407][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:01.407][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:01.407][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:01.408][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:01.408][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:01.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:01.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:01.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:01.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:01.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:01.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:01.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:01.415][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-04-21 18:23:01.416][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:01.417][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:01.417][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-04-21 18:23:01.748][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-04-21 18:23:02.078][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:02.079][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-04-21 18:23:02.084][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-04-21 18:23:02.085][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-04-21 18:23:02.086][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:02.086][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:02.087][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:02.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:02.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:02.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:02.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:02.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:02.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:02.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:02.092][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.092][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.092][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.094][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:02.094][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:02.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.095][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.095][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:02.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:02.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.096][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:02.096][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:02.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.097][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.098][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:02.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:02.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.099][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:02.099][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:02.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.099][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.100][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:02.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:02.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.101][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:02.101][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:02.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.102][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:02.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:02.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.107][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:02.108][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:02.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.108][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.109][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:02.109][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.109][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.110][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:02.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.111][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:02.111][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:02.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.112][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:02.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:02.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.113][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:02.113][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:02.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.114][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.115][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:02.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:02.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.116][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:02.116][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:02.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.117][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.117][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:02.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:02.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.118][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:02.118][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:02.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.119][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.119][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:02.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:02.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:02.131][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-04-21 18:23:02.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:02.140][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[2025-04-21 18:23:02.142][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:02.142][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-21 18:23:02.143][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:02.143][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-21 18:23:02.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:02.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:02.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:02.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:02.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:02.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:02.152][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[2025-04-21 18:23:02.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:02.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:02.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:02.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:02.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:02.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:02.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:02.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:02.159][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-04-21 18:23:02.159][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:02.160][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-04-21 18:23:02.160][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:02.160][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:02.161][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:02.161][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:02.161][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:02.162][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:02.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:02.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:02.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:02.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:02.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:02.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:02.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:02.173][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-04-21 18:23:02.178][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:02.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:02.183][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-04-21 18:23:02.512][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-04-21 18:23:02.842][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:02.843][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-04-21 18:23:02.844][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-04-21 18:23:02.845][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-04-21 18:23:02.846][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:02.846][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:02.846][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:02.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:02.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:02.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:02.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:02.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:02.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:02.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:02.852][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.852][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.852][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.854][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:02.857][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:02.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.859][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.859][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:02.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:02.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.861][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:02.861][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:02.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.862][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.862][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:02.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:02.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.863][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:02.863][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:02.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.864][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:02.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:02.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.865][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:02.866][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:02.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.866][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:02.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:02.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.868][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:02.868][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:02.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.868][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.869][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:02.869][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.870][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.870][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:02.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.871][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:02.871][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:02.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.872][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:02.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:02.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.873][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:02.874][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:02.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.874][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:02.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:02.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.876][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:02.876][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:02.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.877][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.877][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:02.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:02.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.878][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:02.878][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:02.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.879][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.880][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:02.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:02.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:02.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:02.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:02.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:02.895][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-04-21 18:23:02.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:02.905][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[2025-04-21 18:23:02.906][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:02.906][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 18:23:02.907][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:02.907][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-21 18:23:02.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:02.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:02.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:02.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:02.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:02.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:02.911][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.TRACE[2025-04-21 18:23:02.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:02.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:02.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:02.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:02.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:02.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:02.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:02.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:02.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:02.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:02.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:02.918][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-04-21 18:23:02.937][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:02.938][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-04-21 18:23:02.939][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:02.939][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:02.939][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:02.939][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:02.940][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:02.940][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:02.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:02.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:02.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:02.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:02.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:02.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:02.944][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.DEBUG[2025-04-21 18:23:02.945][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-04-21 18:23:02.946][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:02.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:02.946][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-04-21 18:23:03.276][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-04-21 18:23:03.606][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:03.607][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-04-21 18:23:03.609][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-04-21 18:23:03.610][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-04-21 18:23:03.610][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:03.610][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:03.611][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:03.611][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:03.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:03.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:03.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:03.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:03.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:03.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:03.616][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:03.616][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:03.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.616][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:03.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:03.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.618][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:03.618][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:03.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.619][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.619][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:03.619][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:03.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.620][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.620][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:03.621][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:03.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.621][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.621][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:03.622][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:03.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.622][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.622][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:03.623][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:03.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.623][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.624][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:03.624][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:03.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.624][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.625][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:03.625][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:03.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.626][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.626][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:03.626][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:03.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.627][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:03.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:03.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.631][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:03.633][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:03.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.634][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.634][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:03.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:03.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.636][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:03.636][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:03.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.636][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:03.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:03.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:03.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:03.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:03.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:03.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:03.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:03.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:03.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:03.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:03.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:03.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:03.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:03.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:03.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:03.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:03.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:03.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:03.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:03.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:03.648][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-04-21 18:23:03.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:03.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:03.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:03.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:03.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:03.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:03.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:03.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:03.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:03.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:03.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:03.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:03.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:03.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:03.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:03.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:03.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:03.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:03.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:03.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:03.658][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-04-21 18:23:03.658][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:03.658][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-04-21 18:23:03.659][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:03.659][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:03.659][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:03.660][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:03.660][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:03.660][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:03.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:03.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:03.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:03.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:03.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:03.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:03.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:03.668][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-04-21 18:23:03.669][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:03.670][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:03.670][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-04-21 18:23:04.000][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-04-21 18:23:04.335][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:04.336][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-04-21 18:23:04.337][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-04-21 18:23:04.338][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-04-21 18:23:04.339][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:04.339][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:04.339][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:04.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:04.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:04.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:04.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:04.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:04.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:04.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:04.344][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:04.344][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:04.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.345][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:04.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:04.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.346][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:04.347][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:04.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.347][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.348][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:04.348][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:04.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.348][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.349][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:04.349][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:04.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.349][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.350][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:04.350][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:04.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.351][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.351][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:04.351][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:04.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.352][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.352][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:04.352][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:04.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.353][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.353][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:04.353][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:04.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.354][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.354][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:04.354][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:04.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.355][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.355][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:04.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:04.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.357][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:04.357][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:04.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.357][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.358][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:04.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:04.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.359][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:04.359][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:04.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.360][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:04.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:04.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:04.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:04.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:04.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:04.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:04.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:04.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:04.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:04.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:04.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:04.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:04.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:04.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:04.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:04.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:04.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:04.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:04.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:04.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:04.375][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-04-21 18:23:04.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:04.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:04.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:04.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:04.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:04.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:04.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:04.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:04.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:04.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:04.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:04.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:04.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:04.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:04.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:04.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:04.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:04.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:04.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:04.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:04.384][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-04-21 18:23:04.384][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:04.385][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-04-21 18:23:04.385][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:04.386][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:04.386][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:04.386][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:04.386][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:04.387][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:04.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:04.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:04.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:04.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:04.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:04.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:04.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:04.391][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-04-21 18:23:04.392][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:04.395][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:04.396][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-04-21 18:23:04.733][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-04-21 18:23:05.064][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:05.065][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-04-21 18:23:05.066][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-04-21 18:23:05.067][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-04-21 18:23:05.067][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:05.068][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:05.068][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:05.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:05.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:05.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:05.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:05.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:05.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:05.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:05.073][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.073][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.074][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.075][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:05.076][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:05.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.076][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.076][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:05.077][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:05.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.077][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.078][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:05.078][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:05.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.078][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.079][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:05.079][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:05.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.079][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.080][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:05.080][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:05.080][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.081][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.081][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:05.081][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.082][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.082][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:05.082][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:05.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.083][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.083][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:05.083][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:05.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.084][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:05.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:05.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.085][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:05.086][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:05.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.086][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.087][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:05.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:05.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.088][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:05.088][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:05.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.089][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:05.105][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-04-21 18:23:05.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:05.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:05.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:05.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:05.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:05.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:05.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:05.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:05.115][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-04-21 18:23:05.116][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:05.116][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-04-21 18:23:05.117][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:05.117][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:05.117][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:05.118][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:05.118][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:05.118][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:05.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:05.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:05.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:05.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:05.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:05.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:05.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:05.123][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-04-21 18:23:05.124][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:05.124][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:05.125][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-04-21 18:23:05.453][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-04-21 18:23:05.798][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:05.800][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-04-21 18:23:05.805][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-04-21 18:23:05.810][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-04-21 18:23:05.811][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:05.812][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:05.812][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:05.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:05.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:05.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:05.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:05.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:05.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:05.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:05.817][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.818][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.818][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.820][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:05.820][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:05.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.821][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.821][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:05.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:05.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.822][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:05.822][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:05.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.823][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.823][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:05.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:05.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.825][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:05.825][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:05.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.825][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:05.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:05.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.827][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:05.827][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:05.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.827][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:05.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:05.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.829][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:05.829][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:05.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.830][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.830][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:05.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:05.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.831][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:05.831][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.832][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.832][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:05.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.833][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:05.834][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:05.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.834][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:05.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:05.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.835][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:05.836][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:05.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.836][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.837][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:05.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:05.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.838][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:05.838][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:05.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.839][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.842][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:05.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:05.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.843][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:05.844][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:05.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.844][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.845][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:05.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:05.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:05.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:05.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:05.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:05.856][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-04-21 18:23:05.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:05.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:05.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:05.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:05.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:05.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:05.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:05.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:05.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:05.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:05.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:05.863][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-04-21 18:23:05.864][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:05.864][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-04-21 18:23:05.865][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:05.865][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:05.865][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:05.865][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:05.866][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:05.866][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:05.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:05.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:05.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:05.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:05.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:05.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:05.873][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.DEBUG[2025-04-21 18:23:05.874][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-04-21 18:23:05.875][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:05.875][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:05.876][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-04-21 18:23:06.202][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-04-21 18:23:06.538][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-04-21 18:23:06.539][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-04-21 18:23:06.540][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-04-21 18:23:06.541][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-04-21 18:23:06.542][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-04-21 18:23:06.543][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:06.543][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:06.543][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:06.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:06.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:06.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:06.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:06.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:06.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:06.548][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.TRACE[2025-04-21 18:23:06.549][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:06.549][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:06.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.549][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:06.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:06.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.551][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:06.551][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:06.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.552][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.552][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:06.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:06.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.553][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:06.554][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:06.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.554][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.555][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:06.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:06.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.556][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:06.556][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:06.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.556][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:06.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:06.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.558][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:06.558][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:06.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.559][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:06.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:06.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.560][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:06.560][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:06.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.561][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.561][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:06.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:06.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.562][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:06.563][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:06.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.563][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.564][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:06.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:06.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.565][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:06.565][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:06.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.565][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:06.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:06.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.573][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:06.573][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:06.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.574][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:06.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:06.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.575][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:06.576][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:06.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.576][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.577][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:06.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:06.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.578][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:06.578][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:06.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.579][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.579][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:06.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:06.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:06.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:06.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:06.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:06.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:06.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:06.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:06.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:06.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:06.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:06.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:06.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:06.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:06.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:06.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:06.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:06.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:06.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:06.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:06.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:06.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:06.591][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-04-21 18:23:06.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:06.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:06.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:06.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:06.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:06.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:06.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:06.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:06.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:06.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:06.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:06.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:06.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:06.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:06.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:06.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:06.600][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-04-21 18:23:06.600][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:06.600][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-04-21 18:23:06.601][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:06.604][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:06.605][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:06.605][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:06.606][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:06.606][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:06.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:06.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:06.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:06.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:06.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:06.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:06.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:06.611][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-04-21 18:23:06.612][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:06.612][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:06.612][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-04-21 18:23:06.942][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-04-21 18:23:07.279][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-04-21 18:23:07.279][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-04-21 18:23:07.280][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-04-21 18:23:07.281][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-04-21 18:23:07.282][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-04-21 18:23:07.282][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:07.283][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:07.283][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:07.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:07.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:07.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:07.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:07.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:07.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:07.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:07.288][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:07.288][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:07.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.288][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:07.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:07.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.290][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:07.290][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:07.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.291][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.291][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:07.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:07.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.292][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:07.292][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:07.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.293][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.293][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:07.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:07.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.294][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:07.294][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:07.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.295][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:07.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:07.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.296][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:07.296][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:07.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.297][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:07.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:07.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.298][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:07.299][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:07.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.299][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.299][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:07.300][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:07.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.303][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.304][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:07.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:07.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.305][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:07.305][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:07.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.306][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:07.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:07.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.307][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:07.307][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:07.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.308][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:07.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:07.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.309][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:07.310][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:07.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.310][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.310][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:07.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:07.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.311][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:07.312][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:07.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.312][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.312][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:07.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:07.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:07.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:07.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:07.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:07.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:07.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:07.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:07.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:07.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:07.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:07.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:07.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:07.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:07.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:07.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:07.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:07.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:07.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:07.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:07.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:07.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:07.323][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-04-21 18:23:07.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:07.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:07.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:07.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:07.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:07.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:07.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:07.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:07.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:07.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:07.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:07.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:07.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:07.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:07.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:07.332][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[2025-04-21 18:23:07.333][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-04-21 18:23:07.333][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:07.334][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-04-21 18:23:07.334][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:07.334][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:07.335][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:07.335][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:07.335][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:07.335][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:07.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:07.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:07.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:07.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:07.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:07.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:07.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:07.340][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-04-21 18:23:07.340][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:07.341][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:07.341][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-04-21 18:23:07.669][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-04-21 18:23:08.003][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:08.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-04-21 18:23:08.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-04-21 18:23:08.006][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-04-21 18:23:08.007][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:08.007][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:08.007][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:08.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:08.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:08.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:08.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:08.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:08.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:08.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:08.012][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.013][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.013][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.015][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:08.015][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:08.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.016][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.016][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:08.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:08.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.017][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:08.017][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:08.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.018][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:08.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:08.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.019][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:08.020][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:08.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.020][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.021][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:08.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:08.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.022][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:08.022][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:08.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.027][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:08.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:08.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.029][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:08.029][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:08.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.029][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.030][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:08.030][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.030][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.031][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:08.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.032][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:08.032][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:08.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.033][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:08.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:08.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.034][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:08.034][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:08.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.035][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:08.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:08.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.036][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:08.037][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:08.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.037][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.037][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:08.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:08.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.038][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:08.039][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:08.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.039][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.040][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:08.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:08.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:08.051][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-04-21 18:23:08.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:08.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:08.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:08.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:08.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:08.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:08.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:08.061][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[2025-04-21 18:23:08.062][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-04-21 18:23:08.062][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:08.062][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-04-21 18:23:08.063][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:08.063][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:08.063][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:08.064][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:08.064][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:08.064][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:08.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:08.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:08.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:08.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:08.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:08.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:08.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:08.069][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-04-21 18:23:08.070][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:08.070][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:08.070][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-04-21 18:23:08.413][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-04-21 18:23:08.751][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:08.752][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-04-21 18:23:08.753][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-04-21 18:23:08.754][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-04-21 18:23:08.755][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:08.755][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:08.756][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:08.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:08.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:08.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:08.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:08.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:08.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:08.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:08.760][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.761][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.761][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.763][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:08.763][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:08.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.763][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.764][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:08.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:08.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.765][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:08.765][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:08.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.766][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.766][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:08.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:08.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.771][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:08.772][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:08.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.772][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:08.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:08.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.774][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:08.774][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:08.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.775][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:08.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:08.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.776][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:08.776][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:08.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.777][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.777][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:08.778][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.778][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.778][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:08.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.779][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:08.780][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:08.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.780][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:08.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:08.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.782][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:08.782][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:08.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.782][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:08.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:08.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.784][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:08.784][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:08.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.785][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.785][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:08.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:08.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.786][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:08.786][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:08.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.787][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.787][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:08.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:08.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:08.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:08.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:08.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:08.803][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-04-21 18:23:08.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:08.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:08.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:08.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:08.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:08.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:08.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:08.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:08.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:08.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:08.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:08.810][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-04-21 18:23:08.810][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:08.811][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-04-21 18:23:08.811][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:08.811][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:08.812][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:08.812][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:08.812][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:08.813][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:08.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:08.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:08.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:08.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:08.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:08.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:08.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:08.822][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-04-21 18:23:08.823][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:08.823][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:08.824][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-04-21 18:23:09.152][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-04-21 18:23:09.486][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:09.487][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-04-21 18:23:09.488][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-04-21 18:23:09.489][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-04-21 18:23:09.490][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:09.490][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:09.490][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:09.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:09.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:09.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:09.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:09.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:09.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:09.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:09.495][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:09.495][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:09.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.496][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:09.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:09.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.497][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:09.497][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:09.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.501][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.502][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:09.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:09.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.503][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:09.503][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:09.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.504][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.504][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:09.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:09.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.505][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:09.505][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:09.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.506][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:09.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:09.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.507][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:09.507][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:09.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.508][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:09.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:09.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.509][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:09.509][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:09.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.510][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.510][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:09.510][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:09.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.511][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.511][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:09.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:09.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.512][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:09.512][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:09.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.513][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:09.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:09.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.514][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:09.514][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:09.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.515][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:09.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:09.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.516][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:09.517][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:09.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.517][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.517][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:09.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:09.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.518][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:09.519][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:09.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.519][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.519][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:09.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:09.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:09.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:09.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:09.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:09.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:09.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:09.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:09.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:09.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:09.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:09.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:09.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:09.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:09.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:09.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:09.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:09.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:09.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:09.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:09.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:09.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:09.533][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-04-21 18:23:09.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:09.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:09.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:09.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:09.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:09.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:09.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:09.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:09.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:09.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:09.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:09.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:09.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:09.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:09.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:09.539][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[2025-04-21 18:23:09.540][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-04-21 18:23:09.540][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:09.540][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-04-21 18:23:09.541][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:09.541][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:09.541][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:09.542][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:09.542][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:09.542][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:09.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:09.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:09.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:09.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:09.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:09.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:09.546][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[2025-04-21 18:23:09.546][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-04-21 18:23:09.547][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:09.547][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:09.548][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-04-21 18:23:09.900][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-04-21 18:23:10.236][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:10.237][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-04-21 18:23:10.238][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-04-21 18:23:10.239][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-04-21 18:23:10.239][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:10.240][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:10.240][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:10.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:10.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:10.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:10.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:10.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:10.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:10.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:10.249][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:10.249][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:10.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.250][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:10.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:10.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.251][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:10.252][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:10.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.252][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.253][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:10.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:10.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.254][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:10.254][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:10.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.255][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.255][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:10.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:10.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.256][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:10.257][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:10.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.257][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:10.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:10.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.258][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:10.259][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:10.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.259][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:10.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:10.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.261][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:10.261][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:10.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.262][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.262][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:10.263][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:10.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.263][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.263][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:10.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:10.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.265][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:10.265][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:10.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.265][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:10.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:10.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.267][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:10.267][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:10.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.268][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.268][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:10.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:10.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.270][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:10.270][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:10.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.271][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.271][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:10.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:10.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.272][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:10.272][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:10.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.273][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.273][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:10.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:10.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:10.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:10.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:10.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:10.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:10.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:10.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:10.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:10.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:10.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:10.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:10.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:10.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:10.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:10.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:10.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:10.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:10.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:10.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:10.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:10.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:10.289][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-04-21 18:23:10.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:10.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:10.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:10.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:10.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:10.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:10.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:10.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:10.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:10.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:10.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:10.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:10.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:10.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:10.296][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-04-21 18:23:10.296][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:10.297][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-04-21 18:23:10.297][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:10.298][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:10.298][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:10.298][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:10.299][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:10.299][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:10.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:10.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:10.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:10.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:10.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:10.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:10.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:10.303][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-04-21 18:23:10.304][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:10.304][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:10.305][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-04-21 18:23:10.643][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-04-21 18:23:10.975][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:10.976][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-04-21 18:23:10.977][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-04-21 18:23:10.983][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-04-21 18:23:10.984][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:10.984][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:10.985][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:10.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:10.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:10.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:10.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:10.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:10.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:10.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:10.990][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:10.990][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:10.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.990][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:10.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:10.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.992][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:10.992][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:10.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.993][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.993][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:10.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:10.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.994][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:10.994][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:10.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.995][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.995][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:10.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:10.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.996][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:10.996][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:10.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.997][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.997][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:10.997][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:10.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.998][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.998][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:10.998][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:10.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:10.999][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:10.999][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:10.999][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.000][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.000][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:11.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.001][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:11.001][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:11.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.002][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:11.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:11.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.003][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:11.003][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:11.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.004][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:11.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:11.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.005][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:11.005][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:11.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.006][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.006][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:11.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:11.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.007][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:11.008][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:11.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.008][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:11.022][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-04-21 18:23:11.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:11.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:11.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:11.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:11.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:11.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:11.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:11.028][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.DEBUG[2025-04-21 18:23:11.028][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-04-21 18:23:11.028][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:11.029][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-04-21 18:23:11.029][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:11.029][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:11.030][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:11.030][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:11.030][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:11.030][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:11.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:11.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:11.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:11.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:11.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:11.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:11.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:11.035][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-04-21 18:23:11.035][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:11.036][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:11.036][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-04-21 18:23:11.364][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-04-21 18:23:11.694][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:11.695][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-04-21 18:23:11.696][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-04-21 18:23:11.697][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-04-21 18:23:11.700][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:11.702][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:11.703][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:11.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:11.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:11.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:11.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:11.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:11.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:11.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:11.708][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.708][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.708][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.710][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:11.710][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:11.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.711][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.711][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:11.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:11.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.712][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:11.712][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:11.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.713][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.713][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:11.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:11.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.714][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:11.714][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:11.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.715][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.715][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:11.715][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:11.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.716][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.716][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:11.716][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:11.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.717][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.717][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:11.717][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.718][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.718][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:11.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.719][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:11.720][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:11.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.720][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:11.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:11.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.722][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:11.722][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:11.722][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.722][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:11.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:11.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.724][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:11.724][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:11.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.725][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.725][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:11.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:11.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.726][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:11.726][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:11.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.727][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:11.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:11.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:11.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:11.742][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-04-21 18:23:11.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:11.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:11.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:11.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:11.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:11.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:11.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:11.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:11.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:11.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:11.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:11.749][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-04-21 18:23:11.749][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:11.750][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-04-21 18:23:11.750][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:11.750][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:11.751][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:11.751][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:11.751][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:11.752][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:11.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:11.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:11.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:11.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:11.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:11.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:11.756][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[2025-04-21 18:23:11.756][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-04-21 18:23:11.757][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:11.757][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:11.758][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-04-21 18:23:12.085][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-04-21 18:23:12.428][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:12.429][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-04-21 18:23:12.430][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-04-21 18:23:12.431][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-04-21 18:23:12.432][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:12.435][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:12.436][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:12.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:12.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:12.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:12.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:12.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:12.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:12.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:12.441][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:12.442][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:12.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.442][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:12.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:12.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.443][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:12.444][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:12.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.444][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.445][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:12.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:12.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.446][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:12.446][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:12.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.447][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.447][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:12.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:12.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.448][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:12.448][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:12.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.449][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.449][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:12.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:12.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.450][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:12.450][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:12.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.451][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:12.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:12.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.452][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:12.452][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:12.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.453][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.453][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:12.453][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:12.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.454][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.454][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:12.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:12.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.455][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:12.456][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:12.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.456][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:12.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:12.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.458][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:12.458][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:12.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.458][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:12.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:12.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.460][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:12.460][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:12.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.461][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.461][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:12.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:12.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.462][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:12.462][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:12.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.463][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.466][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:12.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:12.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:12.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:12.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:12.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:12.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:12.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:12.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:12.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:12.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:12.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:12.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:12.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:12.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:12.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:12.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:12.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:12.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:12.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:12.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:12.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:12.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:12.479][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-04-21 18:23:12.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:12.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:12.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:12.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:12.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:12.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:12.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:12.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:12.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:12.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:12.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:12.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:12.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:12.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:12.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:12.487][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[2025-04-21 18:23:12.487][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-04-21 18:23:12.487][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:12.488][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-04-21 18:23:12.488][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:12.489][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:12.489][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:12.489][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:12.489][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:12.490][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:12.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:12.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:12.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:12.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:12.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:12.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:12.494][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[2025-04-21 18:23:12.494][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-04-21 18:23:12.495][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:12.496][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:12.496][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-04-21 18:23:12.863][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-04-21 18:23:13.204][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:13.205][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-04-21 18:23:13.206][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-04-21 18:23:13.207][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-04-21 18:23:13.208][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:13.208][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:13.208][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:13.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:13.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:13.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:13.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:13.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:13.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:13.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:13.213][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.213][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.214][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.215][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:13.215][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:13.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.216][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.216][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:13.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:13.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.217][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:13.218][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:13.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.218][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.218][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:13.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:13.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.219][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:13.220][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:13.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.220][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:13.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:13.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.221][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:13.222][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:13.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.222][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.222][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:13.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:13.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.223][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:13.223][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:13.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.224][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.224][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:13.225][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.225][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.225][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:13.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.226][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:13.227][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:13.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.227][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:13.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:13.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.228][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:13.229][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:13.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.229][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:13.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:13.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.234][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:13.234][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:13.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.235][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.235][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:13.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:13.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.236][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:13.237][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:13.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.237][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.237][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:13.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:13.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:13.248][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-04-21 18:23:13.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:13.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:13.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:13.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:13.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:13.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:13.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:13.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:13.255][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-04-21 18:23:13.255][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:13.256][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-04-21 18:23:13.256][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:13.256][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:13.257][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:13.257][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:13.257][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:13.257][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:13.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:13.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:13.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:13.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:13.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:13.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:13.264][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.DEBUG[2025-04-21 18:23:13.265][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-04-21 18:23:13.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:13.266][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:13.266][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-04-21 18:23:13.595][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-04-21 18:23:13.932][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:13.933][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-04-21 18:23:13.934][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-04-21 18:23:13.935][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-04-21 18:23:13.935][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:13.936][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:13.936][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:13.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:13.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:13.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:13.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:13.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:13.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:13.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:13.941][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.941][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.942][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.943][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:13.944][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:13.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.944][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.944][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:13.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:13.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.945][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:13.946][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:13.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.946][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:13.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:13.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.948][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:13.948][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:13.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.948][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:13.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:13.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.950][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:13.950][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:13.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.951][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:13.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:13.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.952][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:13.952][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:13.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.953][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.953][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:13.953][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.954][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.954][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:13.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.955][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:13.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:13.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.956][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:13.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:13.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.962][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:13.963][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:13.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.963][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:13.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:13.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.965][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:13.965][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:13.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.965][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.966][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:13.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:13.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.967][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:13.967][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:13.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.968][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.968][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:13.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:13.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:13.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:13.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:13.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:13.979][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-04-21 18:23:13.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:13.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:13.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:13.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:13.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:13.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:13.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:13.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:13.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:13.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:13.986][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[2025-04-21 18:23:13.986][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-04-21 18:23:13.986][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:13.989][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-04-21 18:23:13.990][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:13.990][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:13.991][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:13.991][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:13.991][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:13.992][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:13.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:13.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:13.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:13.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:13.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:13.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:13.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:13.996][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-04-21 18:23:13.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:13.997][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:13.997][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-04-21 18:23:14.325][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-04-21 18:23:14.660][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:14.661][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-04-21 18:23:14.662][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-04-21 18:23:14.663][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-04-21 18:23:14.664][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:14.664][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:14.665][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:14.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:14.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:14.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:14.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:14.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:14.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:14.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:14.669][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:14.670][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:14.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.670][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:14.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:14.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.672][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:14.672][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:14.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.673][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.673][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:14.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:14.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.674][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:14.674][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:14.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.675][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.675][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:14.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:14.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.676][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:14.676][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:14.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.677][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:14.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:14.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.678][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:14.678][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:14.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.679][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:14.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:14.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.680][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:14.680][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:14.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.684][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.685][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:14.686][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:14.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.686][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.687][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:14.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:14.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.688][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:14.688][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:14.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.688][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:14.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:14.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.690][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:14.690][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:14.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.691][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:14.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:14.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.692][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:14.692][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:14.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.693][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.693][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:14.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:14.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.694][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:14.694][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:14.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.695][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:14.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:14.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:14.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:14.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:14.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:14.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:14.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:14.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:14.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:14.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:14.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:14.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:14.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:14.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:14.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:14.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:14.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:14.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:14.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:14.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:14.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:14.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:14.706][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-04-21 18:23:14.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:14.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:14.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:14.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:14.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:14.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:14.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:14.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:14.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:14.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:14.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:14.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:14.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:14.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:14.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:14.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:14.717][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-04-21 18:23:14.717][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:14.718][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-04-21 18:23:14.718][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:14.718][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:14.719][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:14.719][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:14.719][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:14.719][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:14.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:14.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:14.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:14.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:14.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:14.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:14.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:14.724][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-04-21 18:23:14.725][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:14.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:14.726][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-04-21 18:23:15.054][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-04-21 18:23:15.386][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:15.386][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-04-21 18:23:15.388][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-04-21 18:23:15.388][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-04-21 18:23:15.389][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:15.389][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:15.390][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:15.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:15.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:15.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:15.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:15.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:15.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:15.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:15.394][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:15.394][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:15.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.395][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:15.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:15.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.396][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:15.396][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:15.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.397][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.397][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:15.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:15.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.398][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:15.398][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:15.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.399][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.399][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:15.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:15.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.400][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:15.401][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:15.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.401][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:15.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:15.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.407][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:15.407][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:15.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.408][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.408][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:15.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:15.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.409][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:15.409][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:15.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.410][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.410][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:15.410][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:15.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.411][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.411][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:15.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:15.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.412][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:15.412][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:15.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.413][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:15.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:15.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.414][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:15.414][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:15.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.415][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.415][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:15.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:15.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.416][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:15.416][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:15.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.417][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.417][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:15.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:15.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.418][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:15.418][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:15.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.419][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.419][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:15.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:15.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:15.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:15.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:15.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:15.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:15.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:15.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:15.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:15.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:15.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:15.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:15.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:15.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:15.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:15.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:15.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:15.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:15.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:15.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:15.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:15.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:15.433][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-04-21 18:23:15.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:15.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:15.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:15.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:15.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:15.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:15.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:15.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:15.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:15.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:15.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:15.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:15.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:15.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:15.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:15.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:15.439][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-04-21 18:23:15.440][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:15.440][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-04-21 18:23:15.440][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:15.441][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:15.441][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:15.441][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:15.442][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:15.442][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:15.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:15.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:15.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:15.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:15.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:15.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:15.445][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[2025-04-21 18:23:15.446][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-04-21 18:23:15.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:15.447][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:15.447][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-04-21 18:23:15.781][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-04-21 18:23:16.110][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:16.111][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-04-21 18:23:16.112][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-04-21 18:23:16.113][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-04-21 18:23:16.114][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:16.114][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:16.114][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:16.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:16.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:16.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:16.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:16.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:16.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:16.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:16.119][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.119][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.120][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.121][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:16.121][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:16.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.122][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.122][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:16.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:16.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.126][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:16.128][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:16.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.129][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.129][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:16.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:16.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.130][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:16.131][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:16.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.131][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:16.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:16.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.132][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:16.133][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:16.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.133][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:16.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:16.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.135][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:16.135][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:16.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.135][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.136][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:16.136][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.136][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.137][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:16.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.138][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:16.138][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:16.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.139][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:16.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:16.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.140][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:16.140][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:16.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.141][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:16.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:16.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.142][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:16.142][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:16.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.143][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.143][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:16.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:16.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.144][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:16.144][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:16.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.145][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.145][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:16.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:16.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:16.159][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-04-21 18:23:16.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:16.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:16.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:16.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:16.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:16.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:16.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:16.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:16.165][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-04-21 18:23:16.165][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:16.166][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-04-21 18:23:16.166][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:16.167][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:16.167][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:16.167][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:16.167][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:16.168][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:16.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:16.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:16.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:16.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:16.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:16.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:16.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:16.172][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-04-21 18:23:16.172][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:16.173][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:16.173][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-04-21 18:23:16.507][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-04-21 18:23:16.836][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:16.837][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-04-21 18:23:16.838][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-04-21 18:23:16.839][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-04-21 18:23:16.839][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:16.840][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:16.840][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:16.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:16.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:16.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:16.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:16.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:16.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:16.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:16.844][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.845][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.849][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.851][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:16.851][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:16.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.852][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.852][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:16.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:16.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.853][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:16.853][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:16.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.854][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.854][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:16.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:16.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.855][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:16.855][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:16.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.856][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:16.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:16.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.857][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:16.857][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:16.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.858][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:16.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:16.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.859][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:16.859][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:16.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.860][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.860][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:16.860][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.861][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.861][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:16.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.862][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:16.862][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:16.862][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.863][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:16.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:16.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.864][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:16.864][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:16.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.865][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:16.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:16.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.866][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:16.866][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:16.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.867][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.867][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:16.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:16.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.868][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:16.868][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:16.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.869][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.869][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:16.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:16.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:16.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:16.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:16.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:16.883][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-04-21 18:23:16.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:16.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:16.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:16.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:16.892][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[2025-04-21 18:23:16.893][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:16.893][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:16.894][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-21 18:23:17.313][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-21 18:23:17.723][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:17.724][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-04-21 18:23:17.726][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-04-21 18:23:17.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:17.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:17.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:17.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:17.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:17.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:17.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:17.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:17.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:17.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:17.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:17.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:17.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:17.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:17.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:17.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:17.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:17.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:17.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:17.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:17.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:17.989][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:17.990][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:17.991][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:17.991][private$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[2025-04-21 18:23:18.320][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[2025-04-21 18:23:18.647][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:18.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-04-21 18:23:18.650][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-04-21 18:23:18.651][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[2025-04-21 18:23:18.652][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:18.653][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:18.653][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-21 18:23:18.990][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-21 18:23:19.427][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:19.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-04-21 18:23:19.430][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-04-21 18:23:19.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:19.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:19.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:19.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:19.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:19.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:19.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:19.436][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-04-21 18:23:19.436][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:19.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-04-21 18:23:19.437][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:19.437][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:19.438][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:19.438][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:19.438][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:19.438][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:19.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:19.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:19.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:19.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:19.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:19.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:19.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:19.443][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-04-21 18:23:19.444][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:19.444][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:19.445][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-04-21 18:23:19.773][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-04-21 18:23:20.117][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:20.118][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-04-21 18:23:20.119][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-04-21 18:23:20.120][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-04-21 18:23:20.121][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:20.121][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:20.122][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:20.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.126][FUN] Functions in observer BiodbConfig: [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[2025-04-21 18:23:20.126][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.127][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.127][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.129][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:20.129][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:20.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.130][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.130][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:20.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:20.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.131][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:20.132][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:20.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.132][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.133][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:20.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:20.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.134][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:20.134][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:20.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.135][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.135][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:20.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:20.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.136][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:20.136][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:20.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.137][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.137][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:20.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:20.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.139][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:20.139][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:20.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.139][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.140][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:20.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:20.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.141][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:20.141][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:20.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.142][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.142][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:20.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:20.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.143][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.143][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.144][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.145][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:20.146][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:20.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.146][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.147][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:20.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:20.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.148][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:20.148][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:20.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.149][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.149][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:20.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:20.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.150][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:20.150][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:20.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.151][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.151][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:20.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:20.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.163][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-04-21 18:23:20.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:20.178][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-04-21 18:23:20.178][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:20.179][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-04-21 18:23:20.179][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:20.180][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:20.180][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:20.180][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:20.181][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:20.181][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:20.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:20.186][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-04-21 18:23:20.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:20.187][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:20.188][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-04-21 18:23:20.518][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-04-21 18:23:20.854][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:20.855][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-04-21 18:23:20.856][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-04-21 18:23:20.857][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-04-21 18:23:20.858][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:20.858][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:20.858][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:20.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.862][FUN] Functions in observer BiodbConfig: [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[2025-04-21 18:23:20.864][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.864][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.864][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.866][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:20.866][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:20.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.867][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.867][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:20.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:20.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.868][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:20.869][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:20.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.869][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.869][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:20.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:20.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.871][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:20.871][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:20.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.871][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:20.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:20.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.873][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:20.873][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:20.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.874][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:20.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:20.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.875][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:20.875][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:20.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.876][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.876][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:20.876][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:20.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.877][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.877][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:20.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:20.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.884][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.884][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.885][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.886][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:20.886][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:20.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.887][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:20.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:20.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.888][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:20.889][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:20.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.889][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.889][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:20.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:20.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.890][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:20.891][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:20.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.891][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.891][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:20.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:20.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:20.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:20.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:20.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.903][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-04-21 18:23:20.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.912][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:20.914][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:20.914][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 18:23:20.914][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:20.915][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-21 18:23:20.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:20.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:20.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:20.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:20.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:20.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:20.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:20.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:20.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:20.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:20.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:20.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.056][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:21.057][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:21.057][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 18:23:21.058][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:21.058][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-21 18:23:21.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:21.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:21.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.205][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-21 18:23:21.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-21 18:23:21.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 18:23:21.209][biodb::testThat]
biodb.INFO [2025-04-21 18:23:21.209][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-04-21 18:23:21.210][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:21.210][biodb::testThat]
biodb.TRACE[2025-04-21 18:23:21.211][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-21 18:23:21.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-21 18:23:21.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:21.221][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:21.222][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:21.223][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:21.223][private$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[2025-04-21 18:23:21.552][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[2025-04-21 18:23:21.879][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:21.880][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-04-21 18:23:21.881][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-04-21 18:23:21.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:21.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:21.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:21.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:21.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:21.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:21.886][FUN] Functions in observer BiodbConfig: [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[2025-04-21 18:23:21.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:21.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:21.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:21.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:21.889][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[2025-04-21 18:23:21.890][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:21.891][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:21.891][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-21 18:23:22.218][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-21 18:23:22.550][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:22.551][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-04-21 18:23:22.553][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-04-21 18:23:22.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:22.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:22.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:22.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:22.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:22.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:22.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:22.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:22.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:22.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:22.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:22.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:22.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:22.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:22.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:22.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:22.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:22.567][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 18:23:22.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:22.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:22.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:22.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:22.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:22.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:22.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:22.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.573][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.574][private$selectFields]
biodb.TRACE[2025-04-21 18:23:22.574][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:22.574][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:22.574][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.575][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.575][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.576][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.576][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.576][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.577][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.577][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.577][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.577][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.578][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.578][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.578][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:22.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.585][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-21 18:23:22.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:22.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:22.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:22.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:22.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:22.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:22.588][FUN] Functions in observer BiodbConfig: [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[2025-04-21 18:23:22.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.591][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.591][private$selectFields]
biodb.TRACE[2025-04-21 18:23:22.591][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:22.592][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:22.592][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.592][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.592][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.593][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.593][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.593][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.594][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.594][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.594][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.595][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.595][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.595][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.596][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:22.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.599][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 18:23:22.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:22.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:22.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:22.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:22.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:22.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:22.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:22.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.605][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.605][private$selectFields]
biodb.TRACE[2025-04-21 18:23:22.605][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:22.606][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:22.606][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.606][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.606][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.607][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.607][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.607][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.608][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.608][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.608][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:22.609][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.609][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.609][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.610][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:22.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:22.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.613][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-21 18:23:22.613][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 18:23:22.614][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 18:23:22.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:22.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:22.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:22.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:22.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:22.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:22.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:22.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:22.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:22.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:22.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:22.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:22.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:22.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:22.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:22.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:22.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:22.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:22.647][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:22.649][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:22.649][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:22.650][private$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[2025-04-21 18:23:22.979][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[2025-04-21 18:23:23.353][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:23.354][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-04-21 18:23:23.355][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-04-21 18:23:23.357][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[2025-04-21 18:23:23.358][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:23.358][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:23.359][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-21 18:23:23.688][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-21 18:23:24.016][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:24.017][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-04-21 18:23:24.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-04-21 18:23:24.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.046][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 18:23:24.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.059][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.059][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.060][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.060][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.060][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.060][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.061][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.061][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.061][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.062][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.062][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.062][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.063][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.063][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.063][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.064][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.064][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.067][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-21 18:23:24.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.071][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[2025-04-21 18:23:24.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.089][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.089][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.090][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.090][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.090][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.090][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.091][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.091][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.091][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.092][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.092][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.096][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.096][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.096][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.097][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.097][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.100][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 18:23:24.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.106][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.107][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.107][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.107][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.107][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.107][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.108][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.108][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.109][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.109][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.109][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.109][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.110][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.110][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.110][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.111][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.111][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.115][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-21 18:23:24.115][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 18:23:24.115][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 18:23:24.118][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-21 18:23:24.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-21 18:23:24.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 18:23:24.120][biodb::testThat]
biodb.INFO [2025-04-21 18:23:24.121][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-04-21 18:23:24.121][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:24.121][biodb::testThat]
biodb.TRACE[2025-04-21 18:23:24.122][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-21 18:23:24.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-21 18:23:24.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:24.132][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:24.133][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:24.133][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-21 18:23:24.134][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:24.134][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-21 18:23:24.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.141][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:24.142][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:24.143][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-21 18:23:24.143][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:24.143][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-21 18:23:24.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.156][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 18:23:24.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.162][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.162][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.163][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.163][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.163][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.163][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.164][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.164][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.164][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.165][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.165][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.165][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.166][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.166][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.166][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.167][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.167][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.170][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-21 18:23:24.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.174][FUN] Functions in observer BiodbConfig: [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[2025-04-21 18:23:24.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.176][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.176][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.177][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.177][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.177][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.177][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.178][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.178][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.178][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.179][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.179][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.179][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.179][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.180][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.180][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.180][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.181][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.187][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 18:23:24.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.192][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.193][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.193][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.193][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.193][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.194][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.194][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.194][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.195][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.195][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.195][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.196][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.196][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.196][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.196][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.197][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.197][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.201][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-21 18:23:24.201][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 18:23:24.201][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 18:23:24.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:24.213][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:24.214][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:24.214][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-04-21 18:23:24.215][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:24.215][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-04-21 18:23:24.216][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:24.217][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:24.218][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-04-21 18:23:24.218][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:24.218][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-04-21 18:23:24.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.238][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 18:23:24.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.243][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.243][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.243][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.243][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.244][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.244][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.244][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.245][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.245][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.245][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.246][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.246][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.246][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.246][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.247][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.247][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.247][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.251][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-21 18:23:24.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.254][FUN] Functions in observer BiodbConfig: [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[2025-04-21 18:23:24.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.257][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.257][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.257][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.257][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.258][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.258][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.258][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.259][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.259][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.259][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.260][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.260][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.260][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.260][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.261][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.261][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.261][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.265][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 18:23:24.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.271][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.271][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.271][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.271][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.272][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.272][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.272][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.273][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.273][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.273][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.274][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.274][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.274][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.274][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.275][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.275][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.275][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.279][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-21 18:23:24.279][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 18:23:24.279][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 18:23:24.285][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-21 18:23:24.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-21 18:23:24.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 18:23:24.287][biodb::testThat]
biodb.INFO [2025-04-21 18:23:24.288][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-04-21 18:23:24.288][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:24.288][biodb::testThat]
biodb.TRACE[2025-04-21 18:23:24.289][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-21 18:23:24.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-21 18:23:24.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:24.300][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:24.301][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:24.301][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-21 18:23:24.302][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:24.302][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-21 18:23:24.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.310][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:24.311][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:24.311][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-21 18:23:24.312][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:24.312][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-21 18:23:24.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:24.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.326][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 18:23:24.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.332][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.332][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.332][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.332][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.333][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.333][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.333][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.334][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.334][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.334][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.335][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.335][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.335][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.336][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.336][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.336][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.337][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.340][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-21 18:23:24.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.343][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.TRACE[2025-04-21 18:23:24.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.346][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.346][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.346][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.346][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.347][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.347][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.347][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.348][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.348][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.348][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.349][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.349][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.349][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.349][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.350][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.350][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.350][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.354][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 18:23:24.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.359][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.360][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.360][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.360][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.360][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.361][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.361][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.361][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.362][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.362][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.362][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.363][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.363][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.363][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.363][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.364][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.364][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.368][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-21 18:23:24.368][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 18:23:24.368][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 18:23:24.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:24.384][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:24.385][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:24.385][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-04-21 18:23:24.386][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:24.386][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-04-21 18:23:24.387][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:24.388][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:24.391][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-04-21 18:23:24.392][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:24.392][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-04-21 18:23:24.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.407][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:24.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:24.411][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 18:23:24.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.417][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.417][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.417][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.418][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.418][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.418][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.418][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.419][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.419][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.419][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.420][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.420][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.420][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.421][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.421][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.421][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.422][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.425][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-21 18:23:24.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.428][FUN] Functions in observer BiodbConfig: [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[2025-04-21 18:23:24.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.431][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.431][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.431][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.431][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.432][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.432][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.432][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.433][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.433][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.433][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.434][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.434][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.434][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.434][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.435][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.435][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.435][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.439][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 18:23:24.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:24.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.444][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.444][private$selectFields]
biodb.TRACE[2025-04-21 18:23:24.445][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 18:23:24.445][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 18:23:24.445][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.445][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.446][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.446][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.446][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.447][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.447][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.447][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.448][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 18:23:24.448][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.448][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.449][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.449][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 18:23:24.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:24.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:24.452][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-21 18:23:24.453][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 18:23:24.453][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 18:23:24.459][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-21 18:23:24.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-21 18:23:24.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:24.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 18:23:24.461][biodb::testThat]
biodb.INFO [2025-04-21 18:23:24.462][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-04-21 18:23:24.462][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:24.462][biodb::testThat]
biodb.DEBUG[2025-04-21 18:23:24.463][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-04-21 18:23:24.463][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:24.463][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-04-21 18:23:24.464][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:24.464][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:24.464][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:24.465][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:24.465][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:24.465][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:24.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:24.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:24.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:24.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:24.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:24.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:24.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:24.470][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-04-21 18:23:24.470][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:24.471][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:24.471][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-04-21 18:23:24.802][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-04-21 18:23:25.132][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:25.134][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-04-21 18:23:25.135][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-04-21 18:23:25.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-04-21 18:23:25.137][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:25.137][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:25.137][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:25.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:25.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:25.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:25.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:25.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:25.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:25.141][FUN] Functions in observer BiodbConfig: [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[2025-04-21 18:23:25.142][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:25.143][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:25.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.143][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:25.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:25.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.145][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:25.145][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:25.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.145][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.146][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:25.146][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:25.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.147][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.147][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:25.147][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:25.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.148][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.148][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:25.148][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:25.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.149][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.149][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:25.149][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:25.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.150][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.150][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:25.151][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:25.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.151][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.151][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:25.152][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:25.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.152][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.152][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:25.153][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:25.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.157][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.158][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:25.158][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:25.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.159][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.159][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:25.159][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:25.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.160][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:25.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:25.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:25.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:25.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:25.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:25.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:25.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:25.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:25.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:25.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:25.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:25.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:25.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:25.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:25.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:25.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:25.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:25.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:25.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:25.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:25.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:25.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:25.170][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-04-21 18:23:25.171][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-04-21 18:23:25.174][biodb::testThat]
biodb.INFO [2025-04-21 18:23:25.174][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-04-21 18:23:25.174][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:25.175][biodb::testThat]
biodb.DEBUG[2025-04-21 18:23:25.178][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-04-21 18:23:25.178][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-04-21 18:23:25.179][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-04-21 18:23:25.179][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-04-21 18:23:25.179][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-04-21 18:23:25.180][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:25.180][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:25.180][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:25.181][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:25.181][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:25.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:25.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:25.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:25.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:25.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:25.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:25.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:25.186][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-04-21 18:23:25.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:25.187][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:25.187][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-04-21 18:23:25.521][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-04-21 18:23:25.853][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:25.854][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-04-21 18:23:25.855][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-04-21 18:23:25.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:25.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:25.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:25.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:25.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:25.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:25.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:25.860][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-04-21 18:23:25.861][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:25.861][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:25.861][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-04-21 18:23:26.195][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-04-21 18:23:26.525][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:26.527][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-04-21 18:23:26.528][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-04-21 18:23:26.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:26.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:26.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:26.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:26.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:26.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:26.532][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[2025-04-21 18:23:26.533][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-04-21 18:23:26.534][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:26.534][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:26.534][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-04-21 18:23:26.877][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-04-21 18:23:27.211][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:27.212][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-04-21 18:23:27.213][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-04-21 18:23:27.214][private$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[2025-04-21 18:23:27.215][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:27.215][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-04-21 18:23:27.215][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:27.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:27.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:27.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:27.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:27.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:27.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:27.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:27.220][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.220][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.221][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.223][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:27.223][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:27.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.223][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.224][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:27.224][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:27.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.225][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.225][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:27.225][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:27.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.226][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.226][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:27.226][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:27.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.227][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.227][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:27.227][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:27.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.228][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.228][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:27.229][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:27.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.229][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.229][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:27.230][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:27.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.230][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.231][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:27.231][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:27.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.231][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.232][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:27.232][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:27.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.232][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.233][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:27.233][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:27.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.234][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:27.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:27.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:27.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:27.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:27.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:27.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:27.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:27.245][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.246][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.246][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.248][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:27.248][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:27.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.249][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.249][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:27.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:27.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.250][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:27.250][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:27.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.251][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.251][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:27.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:27.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.252][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:27.252][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:27.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.253][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:27.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:27.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.254][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:27.255][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:27.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.255][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.256][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:27.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:27.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.257][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:27.257][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:27.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.257][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.258][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:27.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:27.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.259][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:27.259][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:27.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.260][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.260][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:27.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:27.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.261][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:27.261][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:27.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.262][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:27.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:27.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.263][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:27.263][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:27.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.264][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:27.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:27.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.265][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:27.266][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:27.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.266][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.267][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:27.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:27.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.268][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:27.268][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:27.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.275][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.275][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:27.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:27.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:27.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:27.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:27.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:27.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:27.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:27.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:27.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 18:23:27.289][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.289][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.289][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.291][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:27.291][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:27.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.292][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.292][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:27.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:27.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.294][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:27.294][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:27.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.294][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:27.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:27.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.296][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:27.296][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:27.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.297][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:27.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:27.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.298][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:27.298][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:27.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.299][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:27.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:27.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.300][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:27.301][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:27.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.301][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.302][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:27.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:27.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.303][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:27.303][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:27.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.304][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.304][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:27.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:27.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.305][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:27.305][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:27.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.306][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:27.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:27.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.308][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:27.308][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:27.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.309][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:27.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:27.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.310][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:27.310][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:27.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.311][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.311][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:27.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:27.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.312][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:27.313][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:27.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.313][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.313][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:27.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:27.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:27.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:27.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:27.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:27.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:27.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:27.332][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-04-21 18:23:27.333][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-04-21 18:23:27.333][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-04-21 18:23:27.338][biodb::testThat]
biodb.INFO [2025-04-21 18:23:27.338][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-04-21 18:23:27.338][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:27.339][biodb::testThat]
biodb.INFO [2025-04-21 18:23:27.347][biodb::testThat]
biodb.INFO [2025-04-21 18:23:27.347][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-04-21 18:23:27.348][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:27.348][biodb::testThat]
biodb.INFO [2025-04-21 18:23:27.350][biodb::testThat]
biodb.INFO [2025-04-21 18:23:27.351][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-04-21 18:23:27.351][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:27.351][biodb::testThat]
biodb.DEBUG[2025-04-21 18:23:27.352][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:27.353][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:27.354][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:27.354][private$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[2025-04-21 18:23:27.732][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[2025-04-21 18:23:28.174][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:28.175][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-04-21 18:23:28.176][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-04-21 18:23:28.181][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:28.181][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:28.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:28.182][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:28.182][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:28.182][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:28.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:28.183][ef$get] fields variable is a list.
biodb.INFO [2025-04-21 18:23:28.183][biodb::testThat]
biodb.INFO [2025-04-21 18:23:28.184][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-04-21 18:23:28.184][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:28.184][biodb::testThat]
biodb.ERROR[2025-04-21 18:23:28.188][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-04-21 18:23:28.193][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-04-21 18:23:28.197][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-21 18:23:28.197][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-21 18:23:28.198][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-21 18:23:28.198][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-21 18:23:28.198][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.199][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.199][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.199][FUN] Functions in observer BiodbConfig: [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 [2025-04-21 18:23:28.207][biodb::testContext]
biodb.INFO [2025-04-21 18:23:28.207][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 18:23:28.208][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-04-21 18:23:28.208][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 18:23:28.208][biodb::testContext]
biodb.INFO [2025-04-21 18:23:28.209][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-21 18:23:28.209][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-21 18:23:28.211][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:23:28.211][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-21 18:23:28.212][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-21 18:23:28.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.212][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-21 18:23:28.213][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-21 18:23:28.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.214][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-21 18:23:28.214][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-21 18:23:28.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.215][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-21 18:23:28.215][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-21 18:23:28.215][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-21 18:23:28.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.216][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-21 18:23:28.217][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-21 18:23:28.217][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-21 18:23:28.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.218][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-21 18:23:28.218][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-21 18:23:28.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.219][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[2025-04-21 18:23:28.219][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-21 18:23:28.219][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-21 18:23:28.219][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-21 18:23:28.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.220][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-21 18:23:28.221][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-21 18:23:28.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.221][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-21 18:23:28.222][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-21 18:23:28.222][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-21 18:23:28.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.223][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-21 18:23:28.223][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-21 18:23:28.223][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-21 18:23:28.224][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-21 18:23:28.224][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-21 18:23:28.224][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-21 18:23:28.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.225][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.DEBUG[2025-04-21 18:23:28.225][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-21 18:23:28.225][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-21 18:23:28.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.226][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-21 18:23:28.226][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-21 18:23:28.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.227][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-21 18:23:28.228][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-21 18:23:28.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.229][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-21 18:23:28.229][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-21 18:23:28.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.230][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-21 18:23:28.230][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-21 18:23:28.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.231][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-21 18:23:28.231][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-21 18:23:28.237][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-21 18:23:28.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.239][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-21 18:23:28.239][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-21 18:23:28.239][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-21 18:23:28.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.241][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-21 18:23:28.241][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.242][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-21 18:23:28.242][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.242][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:28.242][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.243][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.243][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.243][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.243][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 18:23:28.244][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:28.244][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.244][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-21 18:23:28.245][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:28.245][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.245][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.245][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:23:28.245][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:23:28.245][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:23:28.245][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 18:23:28.245][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 18:23:28.246][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:28.246][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:28.246][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:28.246][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:28.247][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:28.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:28.247][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.247][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.248][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:28.248][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:28.248][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.248][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.249][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-21 18:23:28.249][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.249][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 18:23:28.250][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.250][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:28.250][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.251][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.251][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.251][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.251][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 18:23:28.252][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:28.252][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.252][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-21 18:23:28.252][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:28.253][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.253][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.253][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:23:28.253][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:23:28.253][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:23:28.253][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 18:23:28.253][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 18:23:28.253][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:28.254][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:28.254][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:28.254][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:28.254][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:28.255][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:28.255][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.255][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.255][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:28.256][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:28.256][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.256][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.256][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-21 18:23:28.257][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.257][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-21 18:23:28.257][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.258][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:28.258][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.258][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.258][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.259][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.259][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 18:23:28.259][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:28.259][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.260][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-21 18:23:28.260][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:28.260][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.260][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.261][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.261][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:28.261][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:28.261][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:28.262][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:28.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:28.262][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:28.262][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.263][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.263][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:28.263][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:28.263][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.264][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.264][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-21 18:23:28.265][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.265][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 18:23:28.265][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.265][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:28.266][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.266][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.266][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.266][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.267][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 18:23:28.267][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:28.267][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.267][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-21 18:23:28.268][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:28.268][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.268][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.268][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.269][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:28.269][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:28.269][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:28.269][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:28.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:28.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:28.270][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.270][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.271][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:28.271][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:28.271][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.271][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:28.272][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:23:28.272][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.273][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[2025-04-21 18:23:28.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.277][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[2025-04-21 18:23:28.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.278][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[2025-04-21 18:23:28.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.281][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[2025-04-21 18:23:28.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.282][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.DEBUG[2025-04-21 18:23:28.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.285][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[2025-04-21 18:23:28.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.290][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[2025-04-21 18:23:28.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.292][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-21 18:23:28.292][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-21 18:23:28.292][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-21 18:23:28.293][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-21 18:23:28.293][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 18:23:28.294][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-21 18:23:28.294][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-21 18:23:28.294][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-21 18:23:28.295][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-21 18:23:28.295][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-21 18:23:28.295][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 18:23:28.296][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-21 18:23:28.296][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-21 18:23:28.297][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-21 18:23:28.297][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-21 18:23:28.297][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-21 18:23:28.298][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-21 18:23:28.298][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-21 18:23:28.298][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 18:23:28.299][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-21 18:23:28.299][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-21 18:23:28.300][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-21 18:23:28.300][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-21 18:23:28.300][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-21 18:23:28.304][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-21 18:23:28.304][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-21 18:23:28.305][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-21 18:23:28.305][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-21 18:23:28.305][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-21 18:23:28.306][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-21 18:23:28.306][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-21 18:23:28.306][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-21 18:23:28.307][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-21 18:23:28.307][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-21 18:23:28.307][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-21 18:23:28.308][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-21 18:23:28.308][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-21 18:23:28.309][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-21 18:23:28.309][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-21 18:23:28.309][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-21 18:23:28.310][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-21 18:23:28.310][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-21 18:23:28.310][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-21 18:23:28.311][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-21 18:23:28.311][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-21 18:23:28.311][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-21 18:23:28.312][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-21 18:23:28.312][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-21 18:23:28.312][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-21 18:23:28.313][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-21 18:23:28.313][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-21 18:23:28.314][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-21 18:23:28.314][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-21 18:23:28.314][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-21 18:23:28.315][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-21 18:23:28.315][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-21 18:23:28.315][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-21 18:23:28.316][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-21 18:23:28.316][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-21 18:23:28.316][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-21 18:23:28.317][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-21 18:23:28.317][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-21 18:23:28.317][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-21 18:23:28.318][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-21 18:23:28.318][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-21 18:23:28.319][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-21 18:23:28.319][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 18:23:28.319][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 18:23:28.320][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-21 18:23:28.320][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-21 18:23:28.320][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-21 18:23:28.321][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-21 18:23:28.321][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-21 18:23:28.321][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-21 18:23:28.322][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-21 18:23:28.322][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-21 18:23:28.322][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-21 18:23:28.323][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-21 18:23:28.323][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-21 18:23:28.324][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-21 18:23:28.324][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-21 18:23:28.324][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-21 18:23:28.325][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-21 18:23:28.325][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-21 18:23:28.326][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-21 18:23:28.326][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:23:28.326][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.327][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.332][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[2025-04-21 18:23:28.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.343][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[2025-04-21 18:23:28.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.346][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[2025-04-21 18:23:28.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.349][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[2025-04-21 18:23:28.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.352][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[2025-04-21 18:23:28.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:28.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:28.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:28.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:28.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:28.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:28.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:28.355][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-21 18:23:28.355][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-21 18:23:28.356][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.356][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.356][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.357][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:28.357][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.357][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.358][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.358][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-21 18:23:28.358][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-21 18:23:28.358][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-21 18:23:28.359][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-21 18:23:28.360][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:28.360][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:23:28.360][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:23:28.360][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:23:28.360][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-21 18:23:28.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:28.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:28.361][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:28.361][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:28.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:28.362][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:28.362][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:28.362][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-21 18:23:28.362][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:28.362][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:28.363][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:28.363][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-21 18:23:28.363][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-21 18:23:28.363][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 18:23:28.364][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 18:23:28.364][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-21 18:23:28.365][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 18:23:28.365][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 18:23:28.366][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 18:23:28.367][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-21 18:23:28.367][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-21 18:23:28.367][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-21 18:23:28.368][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-21 18:23:28.368][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 18:23:28.368][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 18:23:28.369][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-21 18:23:28.369][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-21 18:23:28.369][biodb::testThat]
biodb.INFO [2025-04-21 18:23:28.370][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-04-21 18:23:28.370][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:28.370][biodb::testThat]
biodb.DEBUG[2025-04-21 18:23:28.372][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-21 18:23:28.373][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:28.373][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:28.373][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-04-21 18:23:28.700][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-04-21 18:23:29.189][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:29.189][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-04-21 18:23:29.191][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-04-21 18:23:29.192][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:29.193][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:29.194][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:29.194][private$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[2025-04-21 18:23:29.521][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[2025-04-21 18:23:29.849][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:29.850][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-04-21 18:23:29.851][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-04-21 18:23:29.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:29.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:29.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:29.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:29.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:29.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:29.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:29.856][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[2025-04-21 18:23:29.857][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:29.857][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:29.858][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-21 18:23:30.188][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-21 18:23:30.518][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:30.519][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-04-21 18:23:30.521][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-04-21 18:23:30.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:30.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:30.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:30.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:30.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:30.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:30.525][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.DEBUG[2025-04-21 18:23:30.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:30.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:30.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:30.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:30.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:30.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:30.541][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[2025-04-21 18:23:30.543][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:30.544][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:30.544][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-21 18:23:30.545][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:30.545][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-21 18:23:30.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:30.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:30.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:30.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:30.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:30.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:30.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:30.549][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:30.550][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:30.551][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-21 18:23:30.551][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:30.551][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-21 18:23:30.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:30.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:30.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:30.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:30.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:30.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:30.555][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[2025-04-21 18:23:30.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:30.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:30.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:30.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:30.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:30.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:30.558][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[2025-04-21 18:23:30.559][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:30.560][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:30.560][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-21 18:23:30.560][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:30.561][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-21 18:23:30.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:30.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:30.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:30.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:30.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:30.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:30.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:30.565][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:30.566][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:30.566][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-21 18:23:30.567][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:30.567][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-21 18:23:30.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:30.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:30.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:30.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:30.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:30.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:30.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:30.571][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:30.572][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:30.572][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:30.573][private$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[2025-04-21 18:23:30.911][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[2025-04-21 18:23:31.239][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:31.240][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-04-21 18:23:31.242][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-04-21 18:23:31.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:31.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:31.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:31.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:31.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:31.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:31.246][FUN] Functions in observer BiodbConfig: [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 [2025-04-21 18:23:31.248][biodb::testThat]
biodb.INFO [2025-04-21 18:23:31.249][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-04-21 18:23:31.249][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:31.249][biodb::testThat]
biodb.DEBUG[2025-04-21 18:23:31.251][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[2025-04-21 18:23:31.252][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:31.252][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:31.253][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-21 18:23:31.583][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-21 18:23:31.916][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:31.917][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-04-21 18:23:31.919][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-04-21 18:23:31.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:31.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:31.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:31.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:31.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:31.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:31.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:31.924][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:31.925][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:31.926][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:31.926][private$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[2025-04-21 18:23:32.255][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[2025-04-21 18:23:32.591][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:32.592][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-04-21 18:23:32.593][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-04-21 18:23:32.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:32.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.598][FUN] Functions in observer BiodbConfig: [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 [2025-04-21 18:23:32.599][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-21 18:23:32.600][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-21 18:23:32.600][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-21 18:23:32.600][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-21 18:23:32.600][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.601][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.601][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.602][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.INFO [2025-04-21 18:23:32.603][biodb::testContext]
biodb.INFO [2025-04-21 18:23:32.603][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 18:23:32.603][biodb::testContext] Test context - Test web services
biodb.INFO [2025-04-21 18:23:32.604][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 18:23:32.604][biodb::testContext]
biodb.INFO [2025-04-21 18:23:32.605][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-21 18:23:32.605][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-21 18:23:32.607][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:23:32.607][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-21 18:23:32.608][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-21 18:23:32.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.609][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-21 18:23:32.609][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-21 18:23:32.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.610][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-21 18:23:32.610][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-21 18:23:32.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.611][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-21 18:23:32.611][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-21 18:23:32.612][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-21 18:23:32.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.612][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-21 18:23:32.613][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-21 18:23:32.613][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-21 18:23:32.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.614][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-21 18:23:32.614][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-21 18:23:32.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.615][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-21 18:23:32.615][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-21 18:23:32.616][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-21 18:23:32.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.617][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-21 18:23:32.617][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-21 18:23:32.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.618][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-21 18:23:32.618][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-21 18:23:32.618][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-21 18:23:32.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.619][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-21 18:23:32.620][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-21 18:23:32.620][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-21 18:23:32.620][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-21 18:23:32.620][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-21 18:23:32.621][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-21 18:23:32.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.621][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.DEBUG[2025-04-21 18:23:32.622][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-21 18:23:32.622][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-21 18:23:32.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.623][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-21 18:23:32.623][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-21 18:23:32.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.624][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[2025-04-21 18:23:32.624][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-21 18:23:32.624][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-21 18:23:32.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.625][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-21 18:23:32.625][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-21 18:23:32.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.626][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[2025-04-21 18:23:32.626][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-21 18:23:32.627][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-21 18:23:32.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.628][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-21 18:23:32.628][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-21 18:23:32.633][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-21 18:23:32.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.634][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[2025-04-21 18:23:32.634][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-21 18:23:32.634][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-21 18:23:32.635][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-21 18:23:32.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.636][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-21 18:23:32.636][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.637][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-21 18:23:32.637][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.637][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:32.637][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.638][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.638][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.638][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.638][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 18:23:32.639][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:32.639][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.639][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-21 18:23:32.639][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:32.640][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.640][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.640][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:23:32.640][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:23:32.640][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:23:32.640][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 18:23:32.640][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 18:23:32.641][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:32.641][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:32.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:32.641][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:32.642][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:32.642][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:32.642][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.642][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.643][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:32.649][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:32.649][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.649][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.650][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-21 18:23:32.650][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.650][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 18:23:32.651][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.651][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:32.651][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.651][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.652][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.652][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.652][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 18:23:32.652][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:32.653][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.653][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-21 18:23:32.653][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:32.653][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.654][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.654][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:23:32.654][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:23:32.654][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:23:32.654][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 18:23:32.654][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 18:23:32.654][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:32.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:32.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:32.655][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:32.655][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:32.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:32.656][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.656][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.656][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:32.656][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:32.657][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.657][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.657][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-21 18:23:32.658][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.658][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-21 18:23:32.658][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.658][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:32.659][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.659][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.659][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.659][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.660][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 18:23:32.660][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:32.660][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.660][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-21 18:23:32.661][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:32.661][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.661][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.661][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.662][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:32.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:32.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:32.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:32.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:32.663][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:32.663][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.663][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.663][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:32.664][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:32.664][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.664][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.664][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-21 18:23:32.665][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.665][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 18:23:32.665][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.665][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:32.666][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.666][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.666][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.666][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.667][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 18:23:32.667][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:32.667][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.667][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-21 18:23:32.668][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:32.668][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.668][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.668][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.669][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:32.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:32.669][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:32.669][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:32.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:32.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:32.670][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.670][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.670][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:32.671][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:32.671][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.671][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:32.671][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:23:32.672][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.672][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[2025-04-21 18:23:32.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.673][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[2025-04-21 18:23:32.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.674][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[2025-04-21 18:23:32.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.678][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[2025-04-21 18:23:32.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.679][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[2025-04-21 18:23:32.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.681][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.DEBUG[2025-04-21 18:23:32.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.682][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[2025-04-21 18:23:32.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.685][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[2025-04-21 18:23:32.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.690][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[2025-04-21 18:23:32.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.691][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.DEBUG[2025-04-21 18:23:32.691][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-21 18:23:32.692][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-21 18:23:32.692][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-21 18:23:32.692][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-21 18:23:32.693][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 18:23:32.693][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-21 18:23:32.693][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-21 18:23:32.694][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-21 18:23:32.694][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-21 18:23:32.695][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-21 18:23:32.695][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 18:23:32.695][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-21 18:23:32.696][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-21 18:23:32.696][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-21 18:23:32.696][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-21 18:23:32.697][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-21 18:23:32.697][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-21 18:23:32.697][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-21 18:23:32.698][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 18:23:32.698][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-21 18:23:32.699][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-21 18:23:32.699][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-21 18:23:32.699][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-21 18:23:32.700][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-21 18:23:32.700][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-21 18:23:32.700][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-21 18:23:32.701][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-21 18:23:32.701][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-21 18:23:32.701][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-21 18:23:32.702][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-21 18:23:32.702][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-21 18:23:32.703][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-21 18:23:32.703][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-21 18:23:32.703][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-21 18:23:32.704][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-21 18:23:32.704][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-21 18:23:32.704][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-21 18:23:32.705][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-21 18:23:32.705][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-21 18:23:32.705][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-21 18:23:32.706][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-21 18:23:32.706][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-21 18:23:32.707][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-21 18:23:32.707][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-21 18:23:32.707][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-21 18:23:32.708][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-21 18:23:32.708][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-21 18:23:32.708][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-21 18:23:32.709][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-21 18:23:32.709][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-21 18:23:32.710][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-21 18:23:32.710][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-21 18:23:32.710][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-21 18:23:32.711][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-21 18:23:32.711][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-21 18:23:32.711][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-21 18:23:32.712][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-21 18:23:32.712][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-21 18:23:32.713][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-21 18:23:32.713][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-21 18:23:32.713][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-21 18:23:32.714][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-21 18:23:32.714][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-21 18:23:32.714][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-21 18:23:32.715][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-21 18:23:32.715][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-21 18:23:32.715][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 18:23:32.716][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 18:23:32.716][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-21 18:23:32.717][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-21 18:23:32.717][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-21 18:23:32.717][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-21 18:23:32.718][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-21 18:23:32.718][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-21 18:23:32.718][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-21 18:23:32.719][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-21 18:23:32.720][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-21 18:23:32.720][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-21 18:23:32.720][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-21 18:23:32.721][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-21 18:23:32.721][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-21 18:23:32.722][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-21 18:23:32.722][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-21 18:23:32.722][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-21 18:23:32.723][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-21 18:23:32.723][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:23:32.724][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.724][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.727][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.DEBUG[2025-04-21 18:23:32.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.730][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.DEBUG[2025-04-21 18:23:32.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.740][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.DEBUG[2025-04-21 18:23:32.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.741][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[2025-04-21 18:23:32.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.742][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.DEBUG[2025-04-21 18:23:32.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.746][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[2025-04-21 18:23:32.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.750][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.DEBUG[2025-04-21 18:23:32.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:32.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:32.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:32.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:32.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:32.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:32.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:32.754][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-21 18:23:32.754][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-21 18:23:32.755][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.755][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.756][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.756][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:32.756][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.756][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.756][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.757][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-21 18:23:32.757][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-21 18:23:32.757][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:32.757][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-21 18:23:32.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-21 18:23:32.759][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:32.759][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:23:32.759][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:23:32.759][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:23:32.759][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-21 18:23:32.759][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:32.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:32.760][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:32.760][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:32.760][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:32.760][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:32.761][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:32.761][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-21 18:23:32.761][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:32.761][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:32.761][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:32.762][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-21 18:23:32.762][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-21 18:23:32.762][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 18:23:32.762][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 18:23:32.763][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-21 18:23:32.763][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 18:23:32.764][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 18:23:32.764][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 18:23:32.765][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-21 18:23:32.766][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-21 18:23:32.766][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-21 18:23:32.766][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-21 18:23:32.767][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 18:23:32.767][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 18:23:32.767][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-21 18:23:32.768][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-21 18:23:32.768][biodb::testThat]
biodb.INFO [2025-04-21 18:23:32.768][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-04-21 18:23:32.769][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:32.769][biodb::testThat]
biodb.DEBUG[2025-04-21 18:23:32.770][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-21 18:23:32.771][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:32.772][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-21 18:23:32.772][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:32.772][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-21 18:23:32.774][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[2025-04-21 18:23:32.775][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:32.775][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:32.776][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-21 18:23:33.108][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-21 18:23:33.436][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:33.437][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-04-21 18:23:33.438][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-04-21 18:23:33.441][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-21 18:23:33.441][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-21 18:23:33.442][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-21 18:23:33.442][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-21 18:23:33.442][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.443][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.443][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-21 18:23:33.445][biodb::testContext]
biodb.INFO [2025-04-21 18:23:33.445][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 18:23:33.445][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-04-21 18:23:33.445][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 18:23:33.446][biodb::testContext]
biodb.INFO [2025-04-21 18:23:33.446][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-21 18:23:33.447][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-21 18:23:33.448][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:23:33.448][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-21 18:23:33.449][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-21 18:23:33.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.449][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[2025-04-21 18:23:33.450][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-21 18:23:33.450][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-21 18:23:33.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.451][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-21 18:23:33.451][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-21 18:23:33.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.452][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.DEBUG[2025-04-21 18:23:33.452][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-21 18:23:33.452][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-21 18:23:33.452][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-21 18:23:33.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.453][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-21 18:23:33.453][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-21 18:23:33.454][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-21 18:23:33.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.455][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-21 18:23:33.455][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-21 18:23:33.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.456][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-21 18:23:33.456][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-21 18:23:33.456][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-21 18:23:33.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.457][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-21 18:23:33.457][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-21 18:23:33.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.458][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-21 18:23:33.458][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-21 18:23:33.459][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-21 18:23:33.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.459][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-21 18:23:33.460][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-21 18:23:33.460][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-21 18:23:33.460][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-21 18:23:33.460][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-21 18:23:33.461][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-21 18:23:33.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.461][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-21 18:23:33.462][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-21 18:23:33.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.462][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[2025-04-21 18:23:33.463][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-21 18:23:33.463][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-21 18:23:33.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.464][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-21 18:23:33.464][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-21 18:23:33.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.465][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-21 18:23:33.465][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-21 18:23:33.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.466][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-21 18:23:33.466][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-21 18:23:33.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.467][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[2025-04-21 18:23:33.467][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-21 18:23:33.467][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-21 18:23:33.474][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-21 18:23:33.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.475][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-21 18:23:33.476][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-21 18:23:33.476][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-21 18:23:33.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.477][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-21 18:23:33.477][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.478][self$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[2025-04-21 18:23:33.478][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.478][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:33.479][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.479][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.479][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.479][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.480][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 18:23:33.480][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:33.480][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.480][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-21 18:23:33.481][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:33.481][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.481][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.481][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:23:33.481][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:23:33.481][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:23:33.481][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 18:23:33.481][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 18:23:33.482][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:33.482][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:33.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:33.482][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:33.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:33.483][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:33.483][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.483][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.484][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:33.484][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:33.484][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.484][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.485][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-21 18:23:33.485][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.486][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 18:23:33.486][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.486][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:33.486][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.487][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.487][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.487][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.487][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 18:23:33.488][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:33.488][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.488][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-21 18:23:33.488][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:33.489][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.489][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.489][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:23:33.489][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:23:33.489][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:23:33.489][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 18:23:33.489][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 18:23:33.489][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:33.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:33.490][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:33.490][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:33.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:33.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:33.491][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.491][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.491][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:33.492][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:33.492][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.492][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.492][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-21 18:23:33.493][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.493][self$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[2025-04-21 18:23:33.493][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.494][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:33.494][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.494][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.499][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.499][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.500][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 18:23:33.500][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:33.500][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.500][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-21 18:23:33.501][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:33.501][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.501][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.501][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.502][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:33.502][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:33.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:33.502][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:33.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:33.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:33.503][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.503][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.504][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:33.504][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:33.504][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.504][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.505][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-21 18:23:33.505][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.505][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 18:23:33.506][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.506][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:33.506][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.506][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.507][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.507][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.507][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 18:23:33.507][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:33.508][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.508][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-21 18:23:33.508][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:33.508][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.509][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.509][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.509][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 18:23:33.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:33.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:33.510][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:33.510][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:33.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:33.511][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.511][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.511][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:33.511][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:33.512][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.512][self$setPropertyValue]
biodb.DEBUG[2025-04-21 18:23:33.512][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:23:33.512][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.514][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[2025-04-21 18:23:33.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.516][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[2025-04-21 18:23:33.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.517][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[2025-04-21 18:23:33.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.518][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[2025-04-21 18:23:33.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.519][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[2025-04-21 18:23:33.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.520][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[2025-04-21 18:23:33.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.521][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.DEBUG[2025-04-21 18:23:33.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.524][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[2025-04-21 18:23:33.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.525][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.DEBUG[2025-04-21 18:23:33.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.526][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.DEBUG[2025-04-21 18:23:33.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.528][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[2025-04-21 18:23:33.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.531][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[2025-04-21 18:23:33.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.532][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[2025-04-21 18:23:33.532][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-21 18:23:33.533][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-21 18:23:33.533][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-21 18:23:33.533][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-21 18:23:33.534][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 18:23:33.534][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-21 18:23:33.534][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-21 18:23:33.535][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-21 18:23:33.535][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-21 18:23:33.536][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-21 18:23:33.536][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 18:23:33.536][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-21 18:23:33.537][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-21 18:23:33.537][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-21 18:23:33.537][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-21 18:23:33.538][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-21 18:23:33.538][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-21 18:23:33.539][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-21 18:23:33.539][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 18:23:33.539][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-21 18:23:33.540][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-21 18:23:33.540][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-21 18:23:33.540][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-21 18:23:33.541][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-21 18:23:33.541][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-21 18:23:33.541][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-21 18:23:33.542][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-21 18:23:33.542][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-21 18:23:33.543][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-21 18:23:33.543][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-21 18:23:33.543][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-21 18:23:33.544][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-21 18:23:33.544][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-21 18:23:33.545][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-21 18:23:33.545][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-21 18:23:33.545][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-21 18:23:33.546][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-21 18:23:33.546][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-21 18:23:33.546][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-21 18:23:33.547][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-21 18:23:33.547][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-21 18:23:33.547][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-21 18:23:33.548][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-21 18:23:33.548][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-21 18:23:33.549][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-21 18:23:33.549][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-21 18:23:33.549][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-21 18:23:33.550][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-21 18:23:33.550][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-21 18:23:33.551][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-21 18:23:33.551][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-21 18:23:33.551][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-21 18:23:33.552][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-21 18:23:33.552][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-21 18:23:33.552][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-21 18:23:33.553][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-21 18:23:33.553][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-21 18:23:33.553][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-21 18:23:33.554][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-21 18:23:33.554][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-21 18:23:33.555][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-21 18:23:33.555][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-21 18:23:33.555][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-21 18:23:33.556][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-21 18:23:33.556][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-21 18:23:33.556][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-21 18:23:33.557][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 18:23:33.557][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 18:23:33.558][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-21 18:23:33.558][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-21 18:23:33.558][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-21 18:23:33.559][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-21 18:23:33.559][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-21 18:23:33.559][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-21 18:23:33.560][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-21 18:23:33.560][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-21 18:23:33.560][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-21 18:23:33.561][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-21 18:23:33.561][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-21 18:23:33.562][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-21 18:23:33.562][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-21 18:23:33.562][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-21 18:23:33.563][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-21 18:23:33.563][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-21 18:23:33.564][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-21 18:23:33.564][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 18:23:33.564][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.565][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.565][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[2025-04-21 18:23:33.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.573][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[2025-04-21 18:23:33.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.579][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.DEBUG[2025-04-21 18:23:33.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.594][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.DEBUG[2025-04-21 18:23:33.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 18:23:33.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.596][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[2025-04-21 18:23:33.597][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-21 18:23:33.597][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-21 18:23:33.598][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.598][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.598][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.598][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 18:23:33.599][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.599][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.599][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.599][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-21 18:23:33.600][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-21 18:23:33.600][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 18:23:33.600][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-21 18:23:33.601][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-21 18:23:33.602][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 18:23:33.602][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 18:23:33.602][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 18:23:33.602][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-21 18:23:33.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:33.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:33.603][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 18:23:33.603][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 18:23:33.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 18:23:33.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 18:23:33.604][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:33.604][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-21 18:23:33.604][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 18:23:33.604][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 18:23:33.604][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-21 18:23:33.605][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-21 18:23:33.605][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-21 18:23:33.605][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 18:23:33.605][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 18:23:33.606][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-21 18:23:33.606][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 18:23:33.607][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 18:23:33.607][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 18:23:33.608][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-21 18:23:33.608][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-21 18:23:33.609][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-21 18:23:33.609][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-21 18:23:33.609][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 18:23:33.610][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 18:23:33.610][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-21 18:23:33.610][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-21 18:23:33.611][biodb::testThat]
biodb.INFO [2025-04-21 18:23:33.611][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-04-21 18:23:33.611][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 18:23:33.611][biodb::testThat]
biodb.DEBUG[2025-04-21 18:23:33.612][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-21 18:23:33.614][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:33.614][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-21 18:23:33.614][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:33.615][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-21 18:23:33.616][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 18:23:33.617][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 18:23:33.617][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-04-21 18:23:33.618][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 18:23:33.618][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-04-21 18:23:33.620][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-04-21 18:23:33.620][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 18:23:33.620][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-04-21 18:23:33.621][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 18:23:33.621][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 18:23:33.621][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 18:23:33.622][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 18:23:33.622][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 18:23:33.622][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 18:23:33.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:33.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:33.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:33.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:33.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:33.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:33.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 18:23:33.626][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-04-21 18:23:33.627][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 18:23:33.627][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 18:23:33.628][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-04-21 18:23:33.959][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-04-21 18:23:35.003][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 18:23:35.003][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-04-21 18:23:35.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-04-21 18:23:35.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-04-21 18:23:35.006][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 18:23:35.006][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 18:23:35.007][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 18:23:35.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 18:23:35.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:35.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:35.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:35.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:35.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:35.010][FUN] Functions in observer BiodbConfig: [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[2025-04-21 18:23:35.012][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:35.012][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:35.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.012][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:35.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:35.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.014][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:35.014][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:35.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.014][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.015][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 18:23:35.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 18:23:35.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.016][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:35.016][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:35.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.017][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.017][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 18:23:35.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 18:23:35.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.018][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 18:23:35.018][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 18:23:35.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.019][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.019][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 18:23:35.019][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 18:23:35.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.020][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.020][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:35.020][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:35.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.021][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.021][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:35.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 18:23:35.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.022][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:35.022][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:35.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.023][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.023][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 18:23:35.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 18:23:35.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.024][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:35.024][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:35.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.025][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:35.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 18:23:35.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.026][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:35.026][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:35.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.027][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 18:23:35.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 18:23:35.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.028][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:35.028][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:35.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.029][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.029][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 18:23:35.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 18:23:35.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.030][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:35.030][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:35.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.031][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.031][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 18:23:35.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 18:23:35.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:35.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:35.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:35.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:35.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:35.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:35.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 18:23:35.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 18:23:35.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:35.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:35.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:35.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:35.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:35.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:35.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:35.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:35.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:35.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:35.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 18:23:35.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 18:23:35.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 18:23:35.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 18:23:35.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 18:23:35.042][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-04-21 18:23:35.043][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-21 18:23:35.043][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-21 18:23:35.044][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-21 18:23:35.044][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-21 18:23:35.044][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 18:23:35.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 18:23:35.044][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 18:23:35.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 18:23:35.045][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 18:23:35.045][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
  5.710   0.390  37.953

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn0.7740.3132.206
ChebiEntry0.1190.0070.130